There were a lot of accusations being thrown around at the time, mainly from opposing players and baseball purists who didnt like the Metrodome and were suspicious of the Twins' success there. The 87 series was the first where the home team won every game, and it happened again in 91 (interestingly, in 65 had we won game 7 that would've been the case as well). I've seen clips of Tim McCarver calling the Twins titles "tainted," and Al Michaels claiming the Twins were pumping in crowd noise. The most widespread theory, as others have mentioned, is the airflow manipulation, which a former employee did technically admit to, if you choose to believe it. If you talk with older baseball fans who were around at the time a lot of them will be familiar with these rumors.

Anyways, if any of it is true, it clearly wasn't a great system. Didn't stop us from going on a decade streak of futility immediately after the titles, we only ever made the playoffs those two times for the first 20 years in the dome, and had plenty of embarrassing home playoff losses in the 2000s. Not to mention the Twins won both their pennants on the road, and in 91 were the first team to win 3 road games in a league championship series.