I think most 6MT BMWs have a 2nd gear synchro issue because its the gear you through the most. The 2nd gear synchro in my 330 6sp ZF gearbox was on its way out. Unless I perfectly rev matched downshifting, it would grind. Fast upshifting would cause grind as well.
A theory that I have heard is that short shift kits AND fast shifting contribute to the 2nd gear synchro wear. If you shorten the throw considerably you cut down the time the synchro has to spool up so wear the synchro faster. Or something like that.
I would ask them to put some fresh fluid in gearbox. That might help. I know in my 330 6MT it does. I usually change when it starts to become notchy and then it feels great for about 5k miles. For my 330, gearbox oil lasts maybe about 15k miles.
2015 F34 328iX GT Glacier Silver
2011 E90 M3 Monte Carlo Blue
2004 E46 M3 Imola Red