Create Moodle course room
Create groups
Add activity Group choice
Limit the number of responses allowed: Enable
General limitation: 0 (default)
Selected Groups: Add available Groups
Click first group
Enter Limit For first group
Click second group
=> number of first group is inserted in second group
=> first group remains empty

No problems with Internet Explorer, Chrome or Opera:
Click first group
Enter Limit For first group
Click second group
=> number of first group is inserted in first group
=> number of second group can be inserted in second group

Tested with:
Firefox ESR 45.0.2 and Firefox ESR 49.0.1
Moodle 3.1.2 (Build: 20160912)
Group choice 1.9.3 for Moodle 2.7-3.1 (Build: 2016100600)