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Since both the barrel and upper are AERO ,I say tell them to make it right.
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OP - you have two ways to go with this. 1) you can send them back to Aero. 2) you can use a dremel by hand to make them line up right if you have a dremel. Personally, I'd just do it myself with a dremel and then use the dremel to also polish it all up nice using the brushes in kit. I don't actually have a 'Dremel' - I have a Master Mechanic kit. Same thing though.
You can fix this by hand also with a round file. A chainsaw sharpening file would work well. File down the lip so that it mates up nice and then polish off will 0000 steel wool.
I like it all to mate up nicely and cleanly so I would make it do so. If the ramps in the receiver were a tiny bit higher than the ramps in the barrel extension it would really be a non issue since the cartridges would chamber without getting hung up. A lip with the barrel extension ramps being a tiny bit higher than the receiver ramps could catch cartridges where the bullet seats in the mouth of the cartridge and cause failures to feed. The solution would be to dremel out or polish out that extra tiny bit of metal at the edge of the feed ramp of the barrel extension.
I'd just do it myself because i do have the tools anyway. I wouldn't want the wait time involved with sending the parts back and getting them back.
The reason these things happen is because most companies don't make all the items themselves. Other companies make parts for them - like barrels.