Overall manual transmission problems in my opinion are less common than problems with automatic transmissions. In fact the problems I have seen in most manual transmissions were actually caused by inexperienced drivers. I actually pity the cars that are used for teaching people how to drive a stick.
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We have seen cases where the BMW transmission will get stuck in second or third gear and will not come out of failsafe mode even if you restart the car. In one case this problem was caused by a dead battery that stored hard codes. Even though the BMW battery was replaced the car remained in Failsafe mode.
Another high-tech manual transmission that has appeared in recent years is Borg Warner's DualTronic, which is used in the Audi TT 3.2L and known as a Direct Shift Gear box (DSG). Like the BMW and Ferrari automated manual gear boxes, this transmission has no clutch pedal and is electrohydraulically controlled.
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The BMW transmission can also have problems that are not related to the fluid or the filter. An example would be if there is difficulty in shifting the transmission into higher gear. A grinding or clicking noise can alert the driver to problems that are happening within the machinery itself.