Here is a collection of common issues that I get report of via email, with instructions about troubleshooting them.
Please note that most of these problems are not directly related to iCleaner. Because of this, this page is divided in two sections (iCleaner related and unrelated).
General rules of thumb:
Most problems with the iCleaner app itself can be solved by reinstalling it. Please make sure you're installing it from one of my official repositories or from the BigBoss repo. Cracked iCleaner packages can cause all sorts of issues, which I won't be supporting.
Most seemingly iCleaner-related side effects (including, but not limited to: safe mode crashes, user interface glitches, screaming children haunting your dreams, etc.) can be solved by respringing, or rebooting your device.
If restarting your device didn't work, try rebooting your device in no Substrate mode: you can do so by rebooting it and holding the "volume up" button until the lockscreen shows up. The device will boot up without Substrate (aka, most of your tweaks won't be working). If your problem goes away while in this mode, then it's very unlikely that iCleaner is the cause of your issue. You may have installed a faulty or incompatible tweak, and it's up to you to track which one is causing your problem and uninstall it. You can use iCleaner Pro's Cydia Substrate addon tool to easily identify which tweak is the culprit.