Why is she doing this?- Opinions Please

Any drastic change in behavior should be seen by the vet. I think this little girl should see one. the fact that she is pooping at night could be two things one she has a stomach problem or two she has some type of anxiety. How long is she alone during the day, that's when she is sleeping, I would excercise her well before bedtime.
If you put her in the crate now after two years she is going to resist, keep the crate in your bedroom, and do not open the door while she is whining, the minute she is quiet go ahead, open it carry her to the litter box just to make sure she doesn't have to use it don't talk or  play put her right in, if she does go in the litterbox treat her.
hopefully one of the trainers will be by w/ some ideas, or correct mine. And welcome to idog, Indy sure is a cutie.

Ditto to all that Deb said, and I just wanted to add a couple of other thoughts. 

Have you changed her diet at all?  and

Do you live in an area where the air masses have been unstable alot lately?  Here in New England we've had hot humid weather wtih alot of weak cold fronts (low pressure areas) sweeping through here and there.  My previous dog who was very sensitive to changes in the atmosphere I know would be absolutely nuts by these weather patterns, and alot of times that bizarre behavior was at night.  She was fine as long as we had a stable high pressure area sitting over us for a long spell, but during the summer that's usually not the case here.  When you said your dog was having night problems, it made me think of my previous dog's problems. 

Make sure she gets a really long, good, exhausting walk in the evening, followed by some good games of fetch and a good run in the yard. 

Hello? I didn't think of that. Yes! I changed her diet about a month ago. She has gone from 2 bowel movements to 3 since. And the third is the one at night. We're in Utah and it's just hot, not too humid.

Kali,

If prior to the diet change this behavior was not occurring, and after the diet change it was, then ..... a conclusion could be made. 

By the way, welcome to i-dog, your little Indy is adorable!!!

Ok, so yes, I changed her diet, but I guess I don't understand why is keeps going #2 in my entry way and not in her litter box- and only at night, (she goes in her box all day long) She has been on the Natural Balance since June 30. (I had to switch from Innova to Natural Balance)
So here's what my husband thought- maybe we should move her litter box to our master bathroom at night and close our bedroom door... and see if she still doesn't use the litter box? He thinks she knows that she won't get praised or a treat for going in the box at night, so she just goes wherever.
I don't know what to do about this... it is frusterating to wake up every morning to have to clean up after her.

I would definitely confine her in some way-- the more you let her practice bad behaviors, the harder it will be to fix them. And no, she has no idea she "did wrong". Dogs pick up on your mood-- she sees you are angry, so she offers submissive behaviors, which  humans often interpret as "looking guilty". She doesn't know why you are angry. As to the not-sleeping, well, try to tire her out really well right before bed. Perhaps a late-night walk or a good fetching game.

Does your pup only use a litter box or just when you are gone or she choses to?  My min pin Izzy uses hers during the day while in her crate and at night while in her crate if needed.  Sometimes she won't use it if there is already something in it.  If she poops in her box, which is actually very rare b/c she does this outside most of the time, she will not poop in it again and will go somewhere in the house if we don't take her out.  I have to make sure if I see poop that I immediately clean it out.  This usually only happens when her tummy is upset and she is going more than normal, or her routine is thrown off and she doesn't go out at her normal times.  She typically goes once in the morning and once in the afternoon.

I think I would crate her at night.  We had the constant crying and whining to get out for awhile also...so bad that Izzy lost her voice the first few days that we had her.  We tried her in the crate in our room and then also in the living room.  After the initial adjusting to the crate, she was much better in the living room b/c in our room she cried all night since she could see us in bed.  Have you tried any special mind toys in the crate with treats?  Also, feeding in the crate can help them like it more too, especially if yours is as food motivated as mine.  Now Izzy RUNS to her crate anytime she sees me even get a treat out...especially when she knows it is time to get back in.  We never have a struggle with it anymore.  I think she actually likes her crate now.  I never thought I would be able to say that. 

At our house, the only litter box Izzy has is in her crate b/c she goes outside otherwise.  A lot of dogs will not go into their crate to use the litter box once they are out.  Mine will, but I have heard that is unusual.  I am not sure where your litter box is placed, but have you thought about getting a second litter box to place elsewhere in your house? 
 
EDA: I hope that all made sense.  I sort of jumped around didn't I! 

Indy is crated durning the day with food and water. Her box is in her bathroom. She goes 90% of the time in her box durning the day/evening and the other 10% during her walk or while we are outside playing. She had not had an accident in a year until this.. my mom has a theory that might be somewhat true.. she thinks that maybe someone came in with something on their shoes that she can smell and it makes her want to go in the entry and she knows in the day she will get a treat for going in her box and at night we are asleep. Our house is only a year old now and so there are not previous smells in the carpet.
Indy loves her crate and goes in there everyday on her own. When I am home all day she sleeps in there too with the door open. She, too, goes running for the crate if I get out the Kong. Some nights she will even get sick of us moving her in bed that she will go sleep in her crate for a couple hours.
So anyway, I guess that is probably the best option is crating her. I think that she only likes the idea of her crate on her terms, that's why she whines when I close the door.
One thing that I am going to try tonight is blocking off the hallway to the entry area where she keeps going. So then she will only have access to a small portion of hallway in front of her bathroom, her bathroom, her bedroom where her crate is and our bedroom. Then I will see if she goes anywhere but the litter box. If she does, I will know that it's not something with that particular entry area (like my mom's theory). If she doesn't then maybe I will leave the baby gate up for a little while and see how it goes. It is especially frustering that we have this new home and thought she was housetrained.
Anyway we'll see how it goes tonight and go from there. Thank you so much for the help!