A few points that come to my mind:
1.) It is likely that many common restaurant inconveniences are not the fault of the server. Food coming late to the table or meals arriving at different times may reflect a kitchen issue rather than a server issue. Even mistakes in the order may be a kitchen issue. Unless the server did something obviously wrong (e.g., rudeness, inattention), I wouldn’t punish him/her for a problem that may well have been out of their control.
2.) A restaurant inconvenience may be a good opportunity to exercise our ability to have hakaras hatov and dan l’kaf zechus; isn’t that worth a few dollars?
3.) A polite word with the server may completely resolve the issue while avoiding the sting and loss of withholding the tip.
4.) I think stronger action (withholding a tip, complaining to the manager, etc.) should only be considered if I felt the problem was significant enough that I didn’t want to return to the restaurant in the future. Since I’ve moved into my present community which has numerous restaurants, that threshold for me has been met only once, and the restaurant closed very shortly after the incident, before I even had the chance to contact the manager.