Limited Battery Capacity
On my B46 the bowthruster battery is fairly small (group 27 I think). I have found that unless I shut off the bowthruster battery switches while under sail this battery is drawn down in parallel with the house battery by the electronics (chartplotter, radar, autopilot, etc.). Over the course of a day's sailing the draw down could be sufficient to essentially drain the battery to the point that the BT would not operate.
The end result was that the BT would cut out while docking at the end of the day. I would then need to raise the engine RPMs to get the alternator output sufficiently high to energize the BT. Since I do not like to dock at high speed (for obvious reasons) I have become hyper-sensitive to the issue and always turn off the BT battery switches immediately after setting the sails.