[quote=@Mikellh Dejax]
The Congregation doesn't actually have very tangible things that can get stolen, even the hardlight ships either dematerialize after use, or cannot be operated by corporeal species.

What about the Congregation and the Builder arrive at an outer rim colony world and then ask the planet for knowledge and trade, but the SF military freaks out and attacks them first?
[/quote]Like I said, either offend you or steal something.
If you don't think there's anything valuable they just take away (keep in mind their tech can deal with non-corporeals to an extend so taking something borderline conceptual is also plausible) then just assume they did something bad to you otherwise and now those people are hiding somewhere deep within the Federation.

Granted, Starfleet or especially local border patrols panicking and firing at you out of reflex is indeed possible. But I don't feel that'd be even remotely enough to bother you.