What to do if you find out that the auxiliary apparatus to be installed is not according to specification?

First you already have noticed that there is some type of problem that needs possible correction; that means you have a general knowledge of the apparatus and the specifications. I would check to assure that there aren't some amended spec's issued. Check with the original contractor/installer and give them your concerns. Notify your immediate supervisor to assure they are aware of your observations. Note: If there is a safety concern, expedite your efforts; warn operators if applicable.