I guess it was flagged because it is a one party opinion that Musk is "bad" (for whatever value of bad). Basically the democrats are throwing a tantrum at Musk because he supports Trump instead of a democrat.
It's not like these government departments were all founded by/hired democrats - these were civil servants following the law as created by congress over decades/centuries. They don't just investigate Musk's companies, they investigate any companies where there is suspicion of illegal activity.