The programmer can set breakpoints guiding the tool to freeze the program execution at specific control locations.
Is the use of guiding in the sentence above correct? If it is correct, what grammar rule makes it correct?
Guide as verb is used to express the following meanings:
- Show the way
- Influence behavior
- Help somebody move
The second point could seem to apply to your case, but in that case guide is used as in the following sentence.
He was always guided by his religious beliefs.
In your case, I agree with @Daniel that causing is the verb I would use.
The programmer can set breakpoints, causing the tool to freeze the program at specific control locations.
You could also make the sentence shorter.
The programmer can set breakpoints which freeze the program at specific control locations.
In the latter sentence, it is not clear that the tool freezes the program; if that is clear from a previous sentence, it is not necessary to make it explicit in that sentence too.