In your first sentence I would use "together" instead of "up". However, in your second example, "together' is understood so the meaning is exactly the same. I like the second better.

I agree with Dan and Fred, and I thought I would add that it would be more common to hear your first sentence phrased this way instead (when spoken): A lot of crap happens when you mix up pills and alcohol, . . . This phrasing would definitely imply that a mistake was made, and not that they were combined (as in 'oops, I thought I was taking a pill, but I swallowed alcohol instead'). After all this analysis, I would guess that your meaning matches the second sentence's structure; wouldn't it be hard to mistake a swallow of alcohol for a pill, or the other way around? I guess that depends on how many pills and how much alcohol you had already consumed . . .

Either is fine. "Mix up" has a second meaning, though, meaning to accidentally mistake one thing for another, or "screw up". The unintended second meaning lends a little power to this statement, though, since it conveys confusion. "Mix up" is a phrasal verb (it has two words); in this particular case the way you split it is probably best: "mix (nouns) up". The last sentence would typically be something like, "I'd never do it again... until next weekend, probably."