A flag is disputed when at least one 10k user sees it in the 10k flag queue and considers it invalid.
So there are actually two ways to get disputed flags in your flagging history. One way is what you've seen; the other way often confuses users just as they've crossed the 10k reputation threshold and have started using the 10k moderation tools (which include the 10k flag queue).
You flag a post, and at least one 10k user thinks your flag is wrong. They "counter-flag" it by flagging it with the Invalid Flag flag reason, which means they think flags on the post "are wrong and should be ignored."
This doesn't necessarily mean your flag was wrong. It doesn't even necessarily mean all the 10k users who reviewed it thought it was wrong.
(Then again, often disputed flags are wrong.)
You might consider asking a moderator or (assuming you're willing to publicize the flag) post on meta to ask specifically about the details of a particular flag. That's sometimes the only way to know for sure what others think of a post and whether or not it should be flagged.
You get 10,000 reputation, and use the flag queue. You see a flag you disagree with.
So you click flag or disagree..., then click Invalid Flag.
In this scenario, *you, the 10k user, will also see this disputed flag in your flagging history*will also see this disputed flag in your flagging history*.
(Some disputed flags only appear in 10k users' flagging histories, because some flag types are generated automatically by the system, and some flags of those types get disputed.)
Whichever of the two ways you get disputed flag--by having your flag disputed, or by disputing someone else's (or an automatically generated) flag, this is not inherently bad.
The number of disputed flags a user has is not counted toward how many flags they get or how high priority their flags appear. (In contrast, your number of helpful and declined flags do affect this...though the practical consequences are not that great--people with really "heavy" flags still often have to wait a significant time for them to be actioned, and flags from users with a relatively high number of declined flags are still seen and considered by moderators and 10k users.)