Both of my EMOs do occasionally not make it home when they display the battery warning alert as well, but it is not happening all the time. Most of the time they are able to make their way home and dock successfully.
There could be due to a number of different reasons why EMO is not making it back in time, one of them could be he is confused/distracted by other lights in the room or a possible battery issue.
@linda shared some very good info regarding EMO’s battery which might also be a factor as well, take a look over here:
Hope this helps Also what firmware version is your EMO on? If he is on 2.0.0 I’d also suggest and wait until the latest firmware 2.1.0/2.1.1 is unsuspended and installing that on your EMO. As there were some improvements made to EMO and Home Station on that latest firmware as well.