The boxes should be designed to hint at the correct end to open. The correct end is the one where you have to get the instructions out, to encourage you to read them. Perhaps you're following the hints?

For the first time you open them that's reasonable, afterwards it's just a faff. I make a mark on the convenient end of the box to open at once I know which it is.

Why not take the instructions out?

Might need them if something changes, if someone else needs the pills, etc.

Surely it makes no difference which end is marked, so long as you always put the pills and instructions back in in the same way?