First if all, which battery charger do you have as different chargers indicate different things? I'm assuming you have a two or three bank charger?
Ok, so have you checked your batteries water level? How old are they?
So on my Dual Pro charger, if my led is flashing red there is usually a battery problem. Had that happen a couple times. Easiest way to trouble shoot this is to switch charger leads from one battery to the other (if able). If the flashing led switches to the other bank, then you have a bad battery. Otherwise it'll be a charger issue. Weakest link are the batteries themselves & would bet you have a bad one. If your TM is a 24 volt system (2 batteries connected in series) there are some folks out there that say to change them as a set. Thought is if you only change one of the two batteries, the older/weaker battery would degrade the performance of the newer battery. Not sure what setup you have but even if you have a 12 volt TM & have 2 batteries connected in parallel, the same thought could apply about changing out the set.