I've replaced broken gears in two other transmissions in the past. Neither were an R3, but the R3 uses the same cassette-type tranny with a spool shifter.
One of them had the shift dogs (the little tabs that extend off the side of the gear that mates it to another beside it upon sliding, via a shift fork) broken off of it from trying to push start the bike and dropping it into gear harshly without the clutch.
The other bike had the 2nd and 3rd gear sets destroyed into crumbled bits that were laying in the bottom of the engine case. Somehow the shift mechanism was able to allow a partial engagement of the 2nd and 3rd gear simultaneously, causing them to fight each other -locking up the transmission.
I straightened the bent primary and countershafts, replaced the gears, straightened two bent forks, checked for engine case cracks, and reassembled.
The bike shifted like butter after that.
The only cause I could imagine was poor machining tolerances on one or multiple parts.
This comes to mind when I realize that many of our Rocket3's parts are made in Thailand -a place not known for industry and manufacturing.
Unless your engine cases were machined wrong, housing the tranny parts off their precise location, I'd have to believe the error was either in the replaced parts or operator mistake.