Mega Man 64 (Nintendo 64) - RetroAchievements/guides GitHub Wiki
Mega Man 64 game page
Total: 21
*Marked have hints in the Spoiler section at the bottom due to being easy to miss
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Story Related
As long as you save whenever you see Data you should be able to notice when these occur with the exception of (4). The game allows you to have many save files so if you make use of them so that even if you miss something you should be able to go back to re-attempt them fairly quickly.
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Side Quest Related
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Time Based (Obviously missable)
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Hard mode Exclusive (All no damage bosses along with the aerial battle and ship battle)
Only expand the following if you don't care