Good evening - I'm Dr. Sara. I'm a licensed veterinarian who works exclusively with dogs and cats. I'm really sorry to hear that you're having a rough start with Allie. I know that it can be really frustrating when you're having house training/potty issues!
While medical issues like diarrhea or a urinary tract infection can cause a pet to need to go to the bathroom more frequently, when I'm seeing both peeing and pooping potty issues at the same time, and the poop looks normal, I'm focusing in on behavioral problems. Still, it's a good idea to have an exam by her vet and have a urine and stool sample checked to make sure there's no medical issues.
Actually, if she doesn't pee and poop in the overnight span, then she is capable of holding it for longer periods of time. When dogs are peeing or pooping in their crates (or the house) while you are away but are able to hold it overnight, then this is very likely a manifestation of anxiety. When dogs are anxious, they will pee and poop - this is part of how they cope with their anxiety. Some other dead giveaways of separation anxiety are barking or whining when you leave, becoming nervous when you leave, reluctance to go into the crate and pacing or panting heavily while you are away.
In your situation, it's a bit difficult to distinguish between separation anxiety vs crate anxiety. If she's OK in the crate in the overnight or when you're otherwise home, then it's probably more separation than crate. Even so, sometimes it's a combination of separation AND crate anxiety, in which case you might find that she does better with an alternate form of confinement like a X-pen (something like this: http://www.chewy.com/dog/midwest-black-e-coat-exercise-pen/dp/45380?utm_source=google-product&utm_medium=cpc&utm_campaign=hg&utm_content=MidWest&utm_term=&gclid=Cj0KEQjwsb-vBRCLj7TvqpGx_MoBEiQALgFGntS9JAgbCffURP1l33yStr9lXLViomoIxkmj9fgCSOwaAocT8P8HAQ), closed into a spare bedroom or bathroom, or baby gated into a more open area like a kitchen. I'm going to also copy over some of my favorite resources on separation anxiety in general.
Separation anxiety has a lot of different facets to treatments. I'm going to include a lengthy article from the ASPCA website as well as a video of a webinar presented by Dr. Melissa Bain, who is a board certified veterinary behaviorist and professor at UC Davis's veterinary school. These are both excellent resources for learning about separation anxiety.
Here is the article: http://https://www.aspca.org/pet-care/virtual-pet-behaviorist/dog-behavior/separation-anxiety
And the webinar: http://www.trainyourdogmonth.com/events/webinars/09/
Basically you are working on ways to both calm and distract her when you are leaving as well as practicing rewarding her for calm behavior. You are also mixing up your cues to make it more difficult for her to tell when you are leaving for a short time vs a longer time. In some cases, anti-anxiety medications can be helpful, but I always caution my clients that it is NOT a replacement for the type of training referenced in the above article. A great way to get started with separation anxiety training is to seek the advice of a local veterinarian or trainer with experience in this area. They can help you put together an action plan based on your pet's individual needs, strengths, and weaknesses while also keeping in mind the strengths and limitations of your home and daily routine. Ask your vet if they do behavior consultations. If they don't do the type of consultation you need, then they should be able to refer you to a trainer that they trust. If they can't, I would start by searching both of the following websites:
Here's an article with info on helping you choose a good trainer:
Please let me know if I can answer any other questions for you :) With your reply we can continue to chat until I've covered all of your concerns :)