I think I put the neck of the bottle slightly "inside" the original one, but not sure if that actually matters. Other than that...not sure. I only had to put it over the empty bulb and let it sit and do its thing.

Try changing graphics scale to 60%, if it's not like that already.

I completed that part with a window scale of 100% (I finished the whole game with no problems with 100% scaling.)

Try clicking on the actual bottle. I found that precise clicking isn't really needed to solve puzzles in Botanicula.

I've tried moving it all over that general area (when it gets too far the bottle starts tilting).
Tried it at 60% and 100%, with and without fullscreen and even tried switching the quality with no joy.
I've tried clicking but it just makes the bottle go back into the cupboard.

Apparently you need to bring it close to the other bottle (when it's perfectly vertical) and then click.

Well after alot of clicking, really tiny mouse movements and more clicking I got it to work.
But I couldn't replicate it after loading it again so I dunno... at least I'm past it.

i kind of had the same problem
but then i placed the whole bottle above the bugs.... suddenly it worked, but i have no idea if this was supposed to work like that :)

common problem on most computers. some people have it some don't. i had it and is no game breaker, don't worry. it is mostly about placement, you will have to unfortunately do a pixel hunt. place it slightly inside the other bottle, or above the bugs are sightly beneath the bottle. again it is a pixel hunt and it differs on most computers, and it is not just this section there are a few more along the game. this is due to the flash coding. you got past it, that is great. if you run into something similar along the way , don't lose hope... pixel hunt a little it will work eventually. it is frustrating but NOT game breaking and given the game, you can even turn an eye on the problem.

have a good one. =)

Put the bottle under the bug container and click on the bug container. Then wait a few seconds