I didnt manage to get a screenshot unfortunatly. They had 2 points from the get go, before any rolls were made at all. I clicked to attack the other squad, and their points displayed as 2, mine 0, before anything else was clicked. This caused me to lose in one of the cursed ties I get with almost every battle.

It does not appear their team has anything special that would cause them to start out with such a huge advantage. There is a unicorn with hold the line and two counterstrike, a symurgh with two counterstrike and song of peace, a dragon with two leadership and fire, and a cockatrice with acid, counterstrike, and regeneration.

This is the first time ive seen this happen, is it a bug or some sneaky mechanic?

If they were on one of the watch towers, they get an automatic +2 defensive points. The area information of the sector should tell you if the area has defensive points.

The squad isnt anywhere near a watch tower and it is a completly normal spot with no special desctiption. Which is why im thinking something weird is going on.

Song of Peace automatically gives you two extra points when defending. It's listed in the gene description. 

Oh, I was looking in the tactics FAQ and didnt see that mentioned. Maybe I should add a symurgh to my roster, what a tricky gene. Thanks for the answer sumatra.

Wow, that's really cool :)