How to be good at coming up with counter example in Topology

I think that it would indeed be odd for people to come up with exotic counterexamples to innocuous conjectures out of nowhere, as you say. Really, what is guiding those counterexamples is a lot of time and experience spent with problems and the material. When you are reading the statement of a theorem, try seeing what happens when you omit a hypothesis to see what may go wrong, and talk to people about it, either here online or in person to share your thoughts. The more you learn, the more connections you will make, and eventually you will begin to see more as you synthesize that knowledge.

For counterexamples, just think: "mission sabotage". In other words, deliberately try to break a given statement.

There are generally no "tips", "tricks", "recipes", or anything else of a universal caliber. (When there are, they are so valued that you will surely run across them.) Mathematics is an art as much as it is a science: one tries, examines for errors, and corrects if needed, as many times as it takes.

The best there is in the direction you are asking is learning a sufficiently rich arsenal of counterexamples. To help with that, Olmsted and Gelbaum have written Counterexamples in Analysis, which is a great and highly beneficial read.