If their is a GCMS and/or NMR of the stuff you use, we can work out what else is in there. Don't forget, they are stating GREATER than 98% i.e. the tolerances between batches allows upto 1.99% to be other compounds. Most likely positional isomers and feedstock.
I don't know where you acquire your material from or what it's intended uses are but if it's intended to be used as a solvent, you can't have stuff left in there which might mess up the reaction. One named route uses 2-Methylbut-3-yn-2-ol as feedstock and that's actually LESS toxic and a more potent hypnotic.
So, while better safe than sorry, I cannot readily think of anything that at 2% is going to represent a greater health risk than the 2-methyl-2-butanol itself.
BTW I'm told it has a simply awful taste and I've noted that some obscure site is selling the carbamate ester of the stuff which I believe is a more potent, longer acting and slightly safer derivative. I forget the specified usage but it seemed... out of place.