First signal is when it's from a person who doesn't have a history of consistent achievements on the public leaderboards. It's not a rule - sometimes there are extremely talented up-and-coming legit runners who go from pretty bad times to WRs in a matter of months (e.g. Derek MacIntyre in Factorio 100%), but their past runs often show steady improvements. Many fake runners pop out of nowhere, or have few/inconsistent top times/PBs.
Second, every serious speedrunning community has people who check the video recording frame-by-frame; other rules usually include a whitelist of mods, posting the save, (for games that have RNG) the seed, and (for games that have replays) the replay. Breaking the rules just outright disqualifies a run. The frame-by-frame videos usually are enough to uncover cheating. E.g. in Minecraft any%, stronghold navigation relies a lot on luck and intuition; but there are visual cues for which room might lead to the end portal, and if a runner doesn't take the split second to look in that direction it's a tell-tale sign they've already scouted the seed.
But yeah, some formerly-respected runners actually put a lot of effort into cheating, and it takes another expert runner (or even the whole community) to bust them. More in-depth for Minecraft: https://www.youtube.com/watch?v=XoEQ8wtawPI