As time2roll suggested, please post the model of surge protector and exactly which lights or message it was providing. Bottom line, if your surge protector isn't "happy" with the power, yes it's a big deal. Some problems have more potential to do great harm than others, but all issues should be resolved.
As others have indicated, 50A service has 1 Neutral, 1 Ground, and 2 110V lines. It's not possible for both to be reversed, but it is possible for L1 and neutral or L2 and neutral to be reversed. If this is what was being indicated, it is a potentially dangerous situation, in terms of threat to life and damage to equipment, for several reasons.