There are several anecdotal issues we've observed thus far, most notably the 4th timeout given to the Seattle Seahawks.
The thing to remember is any referee can make mistakes, and the right call is often not clear and dependent on your perspective. If you could count the number of errant calls, you could perform analysis as to how these refs are performing relative to their ordinary counterparts. As far as I'm aware, no one has undertaken that task.
As for mitigating the influence of the replacements, they are still the referees. The NFL has trained them, and standard tools and procedures like instant replay, challenges, booth reviews are still in place. The replacements have the same mitigation of any ordinary referee.
Most importantly, I would say a team's performance has a greater impact on their
odds of winning than all but the most egregious officiating mistakes. The situation is what it is, and every single team has to make the best of it.