Input clock signal with noise
Very difficult to say why this is happening without more information (scope picture, PCB layout, schematic etc)
What frequency is the signal? Where exactly is it coming from? (the FPGA? or discrete flip flop - not entirely clear from your question) How long is the trace from the pin? What is connected to it?

It could be that it's the way you are testing things is the problem. Have you removed the probe ground clip, wrapped a short wire round the barrel and attached this to the nearest ground point to the signal pin?
If it is really there, then it could be caused by not so great layout of the PCB. Do you have  solid ground/power planes on the board? Is every power pin properly decoupled with the values recommended by the manufacturer?
If you can provide some more info it will be easier to suggest where the problem lies.