e: It happened again with another glad on nightmare, this time clicking on another section, again skipping some (I was testing it, the reason below).
I'm unable to reproduce this. Is there anything in particular you are doing other than skipping sections?

I also ventured with just two other glads, being sure I chose 4. Strangely enough, there's a cooldown on every glad I picked, even though the group consisted of only three glads.
If I am understanding you, you are saying you choose 4 allies but only two accompanied you. Is that correct?