These are binary files. From N-body simulations to haloes. From haloes to merging history trees. From merging history trees to luminosities. The various tests for warnings and errors can relate either to physics or to programming logic.
Errors are definitely to be taken seriously.
Warnings do not necessarily imply that the physics output is wrong, but you should make the effort to understand whether the values being warned about are acceptable or not. This does not mean that the warned-about behaviour only occurs three times. Then use, e.g., emacs mylogfile to see at what point of execution they occurred. If you don't understand the warning, or why a warning is not necessarily an error, feel free to ask me .