Pencil thin barrels will change, that's just weight on the muzzle. Bull barrels even. You are adding a variable pipe on the end of the barrel. For an example: if the can is not perfectly aligned with the bore, you could have a baffle strike, throwing the pill off flight.
Like DNS said, if its drastic, this could be the reason, or the weight at the end of your tube. Harmonics, as mentioned, change, too. If barrel is vibrating at a different frequency than it does unsuppressed, then when the pill is leaving the muzzle, the last and final point of contact with the rifling is at that different frequency, therefore altering where that flight path will terminate compared to unsuppressed.
Happens in pistols, too, friend. I suppressed my 1911 and its not as accurate and POI is different. Its a bit lower, and group opened up. Unsuppressed?? Tight group at 15 yards and POI is POA.