Can my dog get infections from laying in his urine?

My dog is 4 months old and my boyfriend thinks its ok to let the dog stay in the crate for 3 days (I think is completely wrong). He still gets food and water and is let out but sometimes doesn't do anything cause he already peed in the crate. My boyfriend will get mad that he's not doing anything outside and put him back in. This has gone on for three days, and I think the dog will get an infection but he doesn't think so. I gave him a bath and washed everything. He's gotten random scabs on his face, want to know if that could be a sign of anything. We use the crate for when he does pee in the house but if he's locked up for days, peeing when he needs to from his neglect he's never going to learn and will cause behavior problems... So basically, I want to reassure that what I think is right.. that he can get an infection from laying in his pee and also that this can cause behavior problems in the future. I just want input.