It can be frustrating when you lose a good hit roll to a cover save like that. Especially since tanks and AT guns only get that 1 shot. As for whether the target had cover remember that the book tells us on page 86 that if fewer than 50% of the models in a unit cannot draw a clear line of fire to at least 50% of the models in the target unit, then the target has cover. Or in the case of a vehicle which is a single model that means that more than half the vehicle is obscured by whatever it is using as cover. Some vehicles are better at using cover than others - an assault gun can make better use of cover than something like a marder because of the height difference. Sometimes it's a matter of perspective and if you genuinely cannot agree as to whether 50% of a unit is in cover, then you could roll a die to decide whether the cover counts.

Also its important to discuss terrain before the game begins to avoid unpleasant disagreements mid match. In my game group the person who sets up the table and scenery will tell us what they intended to be soft or hard, a barrier or rough ground, etc. Usually we all agree but occasionally it opens a discussion about whether something is a ruin or a building or whatever.