Open DConf Editor > org > mate > power-manager > percentage-(x)
There you'll see the values for percentage-low (set to "9%" -- indicates when battery charge is low); percentage-critical (set to "3%") and percentage-action (set to "2%" -- when the action for percentage-critical is executed).
These are the default values, but why are they so low? I did my homework on lithium ion batteries, and I learned how bad it is to allow your battery to discharge that much. One day, my indicator went to 1% because Ubuntu MATE didn't do anything at the critical level (I'm afraid it still doesn't -- who wants to try that?), and the capacity indicator dropped from 93,6% to 87,3%.
Maybe my sources were wrong and this has nothing to do with the level of charge, but I think you can clarify this subject to me.