td;dr: If you're talking about strictly "when" to counter/hold, it's all about practicing and getting better at it. Watch out for online though, you're probably never be able to get high counter holds on people in online every time.
I notice a lot of times when the match is laggy but at the same time constant, something like what you described happens. Your brain can see the attack coming and under any normal conditions it would work, but with the lag factor involved, you hold, wiff, and then get attacked more. It can be sorta annoying and there isn't really anything you can do about it aside from trying to adjust your timing on the fly. You might have to change your game style and try not to be as reliant on holds.
In offline games it's quite possible to hold a lot of things on reactions, and I feel like with this edition of DOA, i'm able to do that more because the online is better in general, but yeah, sometimes it gets to the point where you literally have to just guess what they are going to do or when they are going to do it.
If you memorize characters strings and the options they can do, it makes things a little bit easier. That's the majority of what learning doa is about I suppose, just learning all the moves/strings. All these new characters confuse the fuu out of me. I don't know what RIg and Sarah and are doing cuz those characters are tall and there kicks look like it could be mid or high and they screw with me a lot just on the mere fact that I don't know there strings.
