The achievements for "Click an enemy X times" are coded to require the exact value. However, the internal click stat can be incremented multiple times per frame before the stat is checked, if you have multiple weapons that tick on the same frame (weapon hits count as clicks).
If you miss any of these achievements, first beat the game so that the only achievements you are missing are for clicks and completing all achievements, unless you're still early enough that resetting doesn't matter. Then reset the game (it may be unresponsive and require a restart afterward), and get the ones you missed. The completion achievement will unlock even if you don't get all the achievements in the same run, but you should back up your save before resetting just in case, at "%localappdata%low\GamesNotToast LTD\Valehona Tap!".
This problem should be easy to avoid by using an autoclicker from the start. The game will take longer if played in the background without one, depending on frequency of check-ins, about 4-8 hours.
