I agree, its very common. When I played more frequently I kept track of players who frequently ally, then would alert their neighbors to my suspicions. I agree, dark start/trade scan only effectively negates this tendency, at least in early game.
As to whether its a problem, it depends on the size of the game. 2 out of 8 is a lot, 2 out of 64 is immaterial.
All of us tend to have opinions as to trustworthy allies from previous games. Where it can disrupt gameplay is when the alliance is unbreakable at the end game, and when number 2 refuses to attack number one. This happens very frequently, and tends to cause end games to die with a whimper.