Really just gotta keep at it. I got a lot of enemies knocked out doing the work from home additional stuff which cut down a bit of the grind. A few notable things I found:
Equip the skill that makes all thrown items home on enemies, this will help prevent missing but you still will have to aim a bit.
Enemies are numbered and grouped, with the boss and shopkeeper being the highest numbered in the group (IE. Zans and Hustlebones will be the last characters in the Styxcoin listings). This can help you find which you're missing.
On assist mode, all regular enemies will die in 1 hit to the blank card. Boss you will still have to whittle down.
Keep whatever enemy you want to capture in a room for last, this will prevent you from accidentally hitting the wrong enemy
Hoverhands unmasked is a bit more annoying than other enemies. The blank card must be thrown at his smallest form for it to capture him.
The final areas had blank cards added in, I believe there are 2 fixed drops in the starting room. This means you'll have to do it twice to get all 3 enemies and the boss.
Final boss has the card hidden a bit, when you walk into the room where you can choose skill it is in a box by the entrance. You also only need to catch phase 1.
The Imposter you only need to capture phase 2 for whatever reason.
Hungryboxes are a card capture. Have fun with that