Nope I'm not at all confused when calling with One Pair on a board with a potential Flush It all depends on hand reading ability, situational factors and playing each hand in a profitable manner
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Starting out I wouldn't worry too much about marginal spots because the "correct" and "wrong" decisions are so close together that you don't really gain that much.
Rather, direct your attention to spots where you might feel lost that also frequently occur. Once you get comfortable with the fundamentals, making the best decision in difficult situations is where you can stand out from the rest of the field.
Now that my rant is over I'll also answer your question at face value. Yes, calling marginal hands is awkward, but the potential for huge mistakes is quite small. When it's a close decision, I'm more inclined to let player(pool) tendencies guide my action so I slightly overfold in the very nitty value heavy environment I play in.
bluff catching is an art, and it does not really matter, if the board is monotone (flush possible) or not. This is just one among many different bluff catching situations, which we will face. For simplicitys sake lets focus on the river, since on earlier streets hands usually have equity, so its not so black and white, when we are bluffcatching, and when we are drawing, and sometimes its a bit of both. But on the river they either have it, or they dont, and you can start by running the following checklist:
1) Could they possibly be betting a worse hand for value?
2) Have you shown weakness in the hand?
3) Are you getting a good price?
4) Are there many busted draws?
5) Have they shown a high propensity to bluff before?
If you cant answer "yes" to at least 2-3 of these questions, then you should probably lean towards folding, and folding will never be a big mistake. In theory people can exploit us, if we fold to much, but as a new player that is rarely going to be something, you need to worry to much about, since most beginners tend to call to much rather than fold to much.
I would not be too worried making a minimal bet. Yes, I would be confused if I shoved, because if I am wrong that would be my tournament life at risk.
If you get called with your min raise, the table sees that you bluff and it could bring you a monster hand later in the tourney when you have a monster hand and they mistakenly assume you are bluffing.
Hand reading, combinatorics, and pot odds all factor into your decision, but the most important thing to understand is the player. Is this player capable of betting on the river with a hand that does not beat top pair? The player pools that we play against are usually very bet honest so if you hold a bluff-catcher only it is not a big mistake to fold.