Yes, there are potential issues with constantly running a system optimizer. Some system optimizers may delete necessary files, leading to instability and errors in the system. It is important to check the settings of any optimizer to make sure that only unnecessary files are deleted and, if possible, to back up critical system files before running the optimizer. Furthermore, some optimizers may be incompatible with certain software or hardware configurations, which can cause further issues. Additionally, running an optimizer too often can lead to performance issues due to excessive disk I/O activity.