Safe to use other docks?

I have an ipod dock built-in to the base of my monitor, designed for use with every iPod generation excluding all the new ones that just came out. (About 3/4 of a year old.) I feel stupid setting up my iPhone dock right next to a built-in not-being-used iPod dock, so today I decided to just try putting my iPhone in the monitor dock. A notification popped up on the iPhone screen telling me that this dock wasn't designed to work with the iPhone or something like that, but otherwise everything worked completely normally. My question is, do you think I'm hurting my iPhone by using a dock that's not designed for it but otherwise works??

it's fine. I have been using the iPhone with my speaker dock and the Dice car kit for awhile now and everything is fine.

The iPhone has a normal dock connector. It shouldn't be a problem.