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i bumped into a moltres so now i can see where it is and try to catch it but it keeps fleeing. I have a wobbuffet with shadow tag but moltres still keeps fleeing before i can even throw a pokeball has my game glitched or am i dong something wrong?
No it is not glitched, it is how it's suppose to be. After about 9 times it will flee to the Sea Spirit Den in Azure Bay where you can finally battle and catch it. Make sure you save before you enter the cave though. It will not show up until you get to about the middle and then it will attack you.