I've just updated the downloads to version 1.1.
If you've already finished the game, you probably don't care unless you're a collector. If you're mid-play-through, only switch to this version if you don't mind starting over because the saves won't work, sorry! If you've downloaded the game and haven't started yet, definitely download this new version.
If you don't know which version you have, check the included .txt file. Version 1.1 has a list of the changes.
There were only five bugs (four quite minor) found, and absolutely zero dead ends (Even though people kept insisting they had found one! There aren't any!!!

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I've fixed the five bugs in this new version. The only bug worth mentioning is the formula for making the first chemical. I'm putting an explanation here because it confused a lot of people but I'm putting it in spoilers to protect people who haven't played yet:
When making the acid, you're instructed to bring two units of purple to a boil. In the code, it checks that you're boiling just purple and then sets a variable that allows you to move onto the next step (adding the yellow). Unfortunately, when fixing a bug in RC1 during beta testing, I mucked up the part of that check that is supposed to check how much purple was in the beaker. And since this had been thoroughly tested before, it didn't get proper testing after I made the change, so it slipped by us!
So, the people that were of the thinking that 2 red + 2 blue = 2 purple were able to successfully complete the acid, when they should have been left with brown. This caused a lot of them to go on to the second chemical with the same mis-interpretation of the chemical recipes and be very confused when it didn't work!
As a side effect, having nothing in the beaker also worked, since it was just checking that there was nothing other than purple in there! So boiling an empty beaker left you with purple in the beaker.
In version 1.1, the acid recipe (rightly) requires two parts purple and one part yellow. Two parts purple is made by mixing one red with one blue, since 1+1=2.
I hope this clears up all confusion on this pretty major bug!
Hopefully the game is all clean now. I've got to say, with all the wacky stuff going on in this game courtesy of Ivy's zany mind, this is the most complicated game I've ever programmed (17665 lines of code if you're counting!) and I'm pleased that so few bugs managed to slip past us!
Thanks for all the kind comments everyone!