I’m not aware of any hard issues (backward incompatibilities, bugs, etc.) between PhoneGap 2.4.0 and 2.5.0 but there are several other factors to keep in mind:
1. PhoneGap periodically drops support for older versions of iOS. For example iOS 4.2 was the oldest supported after PhoneGap 2.0.0.
PhoneGap 2.5 similarly requires iOS 5 and XCode 4.5, which some developers may be unable to use if they want to keep supporting older iOS devices or if their development laptop is running a Mac OS older than Lion
2. Upgrading PhoneGap apps can also be a pain, especially on iOS. The “easiest” way right now is to generate a new project and manually copy the www folder over, and replace the phonegap-2.X.X.js file with the appropriate version, but if you are running native hybrids or relying on plugins, that may not be enough. In some cases, you will also need to update the AppDelegate.m or add lines to config.xml, amongst other tweaks. There are step by step guides on how to upgrade on the PhoneGap website:
http://docs.phonegap.com/en/2.5.0/guide_upgrading_ios_index.md.html
Cheers,
Tim