Like Mark, I'm guessing your problem is with SMT parts on the top side, the solder is re-melting and some of the parts are moving around during when the board is being wave soldered.
When I had some training on thru hole wave soldering way back when, the target was 3 seconds of contact with solder when you wave solder. If the component leads have more than 3 seconds of contact, the top side of the board might get hot enough to reflow the solder joints on SMT parts on top. The glass plate I use is a special tempered glass with grid lines on it. It is called a Lev Check, made by Hexacon.
When the glass is over the wave solder you can get an idea of how big the contact area is, and how even it is. Handle the glass very carefully while it is hot. Adjust your conveyor speed to get 3 seconds of solder contact. If you are still having a problem you will need to check the preheat temperatures, you may be getting the boards too hot before they get to the wave solder.
Good luck, Mike F
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