Hmm. I've been thinking about this one for a while and I'm not sure what I think exactly. Here's my opinion but it's just an opinion and hopefully someone else will also jump on who has experience.
When your LO fights going to bed at night, I wouldn't consider that a night terror or nightmare. To me that sounds like a routine issue, a developmental issue or SA, teething, etc. But I'm quite sure it's not a terror (from what I have read) or nightmare. I tend to think those happen more in the night after a period of sleep. Could he maybe be scared?
As far as when your LO wakes up, it sounds like it could be a night terror but more of a nightmare to me. (I'm basing this off what I read on your post) When my LO has a night terror, he thrashed and kicks so much that I can't even hold onto him sometimes. His screams are high pitched and he's an absolute mess for at least 10 minutes. When I put him in his crib, he will throw himself around, bang his head into the side, etc. It's almost a little violent! I am sure there are varrying degrees of terrors but in my experience, they are very severe. Once I get him snapped out if it and calmed down, he goes down pretty easily. Does your LO do any of these things when he wakes?
On the otherhand, when my LO has a nightmare he screams out and acts scared and clingy. He's comforted the minute I hold him and usually needs a little AP to get back to sleep. I think that's what you might be experiencing. If it is a nightmare, then there is probably something that happened to him that days or a few days back. Since DS started his terrors I've been very careful to observe my LOs day and watch for anything he might see or hear that is disturbing. Usually when he has a nightmare, I can look back to something that happened very easily. Whereas I notice with the terrors that they seem to correlate with a routine issue or OT or OS. If you had to stay with your LO for 3 hours last night and you don't think it has to do with routine or teething, etc. I would say it was more of him being scared or some SA.
You might consider posting your routine and seeing if maybe that could be it? 3 hours is a long time to take for a LO to settle. Something is definitely up.
HTH!!