The tall enemies need to be charged on for 2 or 3 beats depending on their height, but what you're describing sounds like it's maybe a bug! There are some timing issues in different environments and we didn't have a chance to iron out of all them for the jam.
Out of curiosity, what browser/OS did you run into this in? (FWIW, we had our best luck in Chrome, and issues in Safari and the HTML5 game launcher bundled with Itch.)