Poker math confused..

Right, so I'm starting to try and understand some of the more simple math behind poker. Pot odds and hand odds, I understand that to make a long term winning play I must be calling with smaller hand odds to pot odds. Ie getting 4:1 to hit my flush and getting 5:1 pot odds, this would be a winning call to see the turn.

But say your playing high pair and someone gives you bad pot odds to call? I've been in situations where in the long run its a loosing call as i might be getting 4:1 and 3:1 pot odds, but been pretty sure I've had the best hand.

I'm not sure if i've explained this problem out as well as it is in my head but if anyone can make any sense of this and explain to me would be much appreciated

If you have the best hand (if it really the best hand) you just cant have bad pot odds: you dont have to improve your hand to win, so what are you compering with pot odds exactly?
Trying figuring out of your hand is the best or just the second is other problem☺