Title of the topic basically says it all. In the rules it says that you can only bring one card out of shadows per phase, but I am wondering if that only applies to the window where you bring out cards from shadows at the beginning of each phase. Does this also apply to cards like meera or guardian wolf?

Well, let's look at a parallel situation. The rules say you can only play characters, locations, and attachments from your hand while you are the active player during the Marshaling phase. But there are a lot of card effects that allow you to put characters, locations, and attachments into play from your hand at other times and in other phases. The Marshaling phase rule does not limit these card effects because they are two entirely different mechanics - a game mechanic and a card effect.

The same thing is going on with Shadows. The "one Shadow card per phase" limit is placed on the game mechanic. It has no impact on card effects that bring cards out of Shadows at other times than at the beginning of the phase.

You can only bring one card out of Shadows in the Challenge phase using the standard start-of-phase mechanic. But you can trigger as many card effects that bring cards out of Shadows in the Challenge phase as you can pay for.