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So how do chaos cults get started on imperium planets, if the inquisition is always on the look out woudnt they stop the cult before it starts going.

There quite simply aren't that many Inquisitors around, though even if the Imperium actually had one per planet (which they don't), a planet is huge and has lots of hiding spots. Influence amongst locals, and with it access to considerable resources, as well as the thin line between sanctioned worship (of the Emperor) and heretical beliefs further make their job rather difficult. I'd imagine many cults start out ostensibly praising Him-on-Earth, but ultimately corrupting their members towards Chaos. Other cults are started specifically because the population is already on the breaking point of rebellion due to ongoing repression. One approach makes a cult's true purpose harder to identify whilst the other grants support by the populace, which can be organised into an ad-hoc insurgency as needed. And then there's the third option, which is corrupted nobility, which of course would have a lot of pull with planetary authorities, further delaying Imperial response.

The first ones to notice that something is wrong usually isn't actually the Inquisition but the Ecclesiarchy due to its local preachers (due to their contacts to the population), who then forward this information to the Inquisitors.

The Inquisition is far from omnipresent.

Just like how underground/insurgent/terrorist movements begin here. The disenfranchised and militant either get together and secretly organize the cult or an outside force infiltrates the area (such as Alpha Legion).

Combine with the fact that the Imperium is severely underpoliced and it isn't that hard at all.

There's always some dark hole for people to hide in.

The Inquisition also has better things to do then chase down every single chaos cult. 95% are just small timers that will never amount to anything serious.

Local authorities, Ecclesiarchy, Arbites, and Inquisition has the most to least responsibility (in that order) uncovering cultist activity as it is.

Chaos is insidious and easy to hide. Even if chaos members are known to authorities as criminals, it's hard to prove chaos taint... unless you have tentacles. By that stage of chaos worship you're probably more learned, more powerful and better able to hide yourself.