the paintball guns were probably pepperball guns. they shoot a paintball filled with a dry pepper powder that burns the eyes, nose, throat, and skin on contact. it also shoots at about 300+ fps and arround 11 balls per second. it not lethal or truly dangerous but it is certainly painful... its was developed for police and riot control.
http://www.pepperball.com/law/products.html
I'm interested to see how the facts play out so I'll reserve comment. But I know that if you dropped a bunch of soldiers on my boat in the middle of the night we're gonna have some problems. Especially if I'm in international waters (which seems to be the one fact neither side disputes at this point). And what is the deal with the soldiers carrying paintball guns? What is the purpose of that, tag? Seems like it just invites a conflict from the other side when they see any type of gun pointing at them (at night no less).