I just recently picked up my dog from the local animal shelter yesterday. The puppy is 5 months old and was spayed yesterday. I brought her home and started to crate train. The puppy is very good about going inside her crate on her own after I have taken her outside and brought her back inside. But when I need to go some where, I usually close the crate to confine her so she doesn't run around my room or the house unattended. I put her in her crate today and closed it so I could go do some work outside, but she started to whimper a whole lot. I tried ignore it and hope she would stop after a little bit of time, but I have a feeling she has separation anxiety due to factors such as living in a new environment, recovering from recent surgery, a new owner, etc.

Is it common for puppies recently adopted from the shelter to act like this and usually how long does it take for the puppy to get over this stage with proper socialization and training?

Yes, it is quite common for a dog to whimper and cry when left in a crate, regardless of the dog's circumstance. Your dog does not have separation anxiety. Separation anxiety is far more complex to diagnose. What you do have is a dog that needs to be taught why the crate is a wonderful place and I suggest you do so by leaving your dog a frozen stuffed Kong with each departure. If you do this often enough your dog may come to learn that you leaving is a predictor for something enjoyable, like food. As your dog gets older you'll also want to exercise your dog before leaving her for a long period of time, and I don't recommend using a crate for over 4 hours at a time. And yes, any time a dog is in a new environment or circumstance, you have to expect a digression in behavior and training. A new home, surgery, and new owner is stressful to a young pup, so do what you can to moderate that stress.

How long it will take for your dog to adjust depends on the individual dog and how well and committed you are in helping your dog to adjust.

Thank you for the advice. I do all of the above and make the dog understand that the crate is a good place to be. I place treats in there when it's not looking so it comes back to check the crate for any hidden treats once in awhile. I pet it and praise it inside the crate until it is relaxed or napping then I close the door while I continue to do all of this and walk away to leave or do or nothings where I can't monitor the dog. After 2 days of doing this, the dog whimpers when I leave but it stops after about 5-10 minutes, which is pretty good now. I've been walking it around the house and backyard a little bit, then playing with it if it doesn't seem tired enough before crating it. Moving along, now for the actual feeding/taking out.

I work the night shift so I pretty much have most of the day to train the dog unless I'm sleeping or out running some errands.

I leave for work around 12 midnight and get back around 8 or 9. So it's hopefully in there for about 8 hours sleeping. At night before I leave, I take the dog out to do it's business and try to exercise and tire out the dog as much as possible so it can sleep through the night until I get home in the morning. When I take out it out to do it's business or do some activity, it sometimes does what it needs to do or it doesn't so I bring the puppy back in and try again later. Sometimes it doesn't even go at all after many attempts and I have to end up putting it inside it's crate to sleep so I can sleep or leave. When I get home, there's usually a puddle inside the crate. The dog is usually very excited and going all crazy inside the crate because I just came home. Am I usually supposed to wait for it to calm down and let it out or let it out right away because 1) it's moving around inside it's own pee and 2) it probably has to do a #2 outside. I usually try to wait for it to calm down then let it out for #2 and it does that outside and I praise it and give it a treat then bring it back in and play with it or let it run around while I watch it. Basically, I'm trying to do everything according to what I've read and from advice from many different dog owners that I know. It's only been about 4 days since I've gotten the puppy. Maybe I am just expecting too much since it usually takes a lot more time to properly train the puppy. I am just concerned because the dog has to wait inside it's own pee until I get home and it hasn't had a bath for a few days because I can't bathe it for 7-10 days after it got spayed due to it's sutures and surgical glue.

I know it's a big wall of text, sorry for that. But I'm really trying to start off on the right foot and train this dog to be properly house trained.

Any advice or tips from anyone would be highly appreciated.

Thanks

As far as cleaning goes, try cleaning it with a wet towel...

I wish you patience and Love for your new friend. I'm sure you'll find ways to deal with all problems in due time.