Our dog only barks when my husband pets him at night?

We adopted Rocky (male, probably about 6 years old) from the shelter two weeks ago. He had been staying with us for about 3 weeks before that to try out everything on a sleepover. So about 5 weeks with us total. He is super reactive with other dogs. We have been working with a trainer on that and it's going pretty well.

What we've noticed the last few days is that when my husband goes to pet him at nighttime, Rocky yelps/barks. This is already when Rocky is cuddled up with me on the couch, so it's not like Rocky wants attention. He regularly hangs out cuddling my husband during the daytime, and gets and asked to be pet all day long from him. This is only in the last few days it is happening.

What we know about Rocky's history is that his first family had him get into a scuffle with another dog, and a human got bit when taking them apart. He had 11 teeth missing and had to get 7 or 8 more pulled for chipped/loose. He seemed to have had a skull or jaw fracture at some time because his snout is crooked. He was in fosters on and off for the last two and a half years. Vet checked him out and said he's looking mostly good for all that going on. He seems to be blind or losing sight in one of his eyes.

I try to show lots of affection to my husband and also to my dog, and Rocky doesn't seem to mind it at all. No resource guarding, no barking for attention, nothing. Outside of his barking at other dogs, this is the first thing that seemed strange to us.

What should we do? Is there any way I can encourage him with my husband? Husband was always nervous around dogs so he agreed to Rocky because he got so well and was very low energy all the time.

Anyway. Want to make sure we're doing all we can for him. Thanks.