Are you asking about athletics, or in general?

The Guinness book of records has some incredibly stupid ones, like “most marmite eaten in one minute” and “longest beard”. I don’t know of those are controversial, but they sure are stupid.

I’m asking about athletics.

Ben Jonson 100 meter dash. Lance Armstrong tour d’ France. Both were juicing.

^Yeah I know Lance Armstrong controversy.

There’s a wee bit of contention regarding the most home runs in a single MLB season.

World records set at the 1968 Olympics in Mexico City were disputed due to altitude.

Super suits were a big deal in swimming for a while, since they were slick, compressive, and buoyant. I think the rules changed a few times because of them.

When you get into auto racing, pretty much every season, and every record is a controversy of some sort.

Not exactly a record per se, but in chess there was some controversy over FIDE awarding Nona Gaprindashvili the title of Grand Master (making her the first woman GM), in 1978, short of the standard system of qualifying for the title by achieving three “norms” (which are, basically, certain performance benchmarks). In 1991 Susan Polgar became the first woman to achieve the GM title via the standard norms.