Oh dear. Yes, that is probably not an ideal way to transport a bird! Did you quarantine your new roo away from your other birds?
There are two possibilities that immediately spring to mind:
1) He was injured, or
2) Transporting him caused him stress, and "hidden" problems are often opportunistic of this and will show themselves suddenly when a bird becomes stressed.
If he were mine, I'd isolate him in a quiet area, such as in a kennel or large crate, so that he can rest. Observe him carefully. If he seems to be in pain, you can offer him painkiller... I actually just posted about this so I will give you a link to the dosages:
https://www.backyardchickens.com/t/875023/hen-not-walking-for-4-days#post_13300823
While he is isolated and resting (hopefully) observe him carefully and let us know if you see any other symptoms. I hope it is just a minor injury and that he will be well soon!
I truly hope you quarantined him in case he is sick and not just injured! I'd hate for you to accidentally spread a disease in your flock.