You should use "mix up". And "confuse" is also good. I often mix up the words shirt and skirt. <-- best I often mix up the word shirt with/and the word skirt. I often confuse the words shirt and skirt. <-- best I often confuse the word shirt with/and the word skirt.

Maybe it's just me, but "mix" by itself sounds deliberate. I'd use "mix up". Even better: "get ___ and ___ mixed" I often get (the words) shirt and skirt mixed.

Yes, you can say this several ways: I often mix the words shirt and skirt I often mix the word shirt and the word skirt I often confuse the words shirt and skirt I often confuse the word shirt and the word skirt