The simple answer is "no". You can go ahead and use the fuel. You will constantly accumulate some water in the fuel--sort of the nature of where you boat, the temp, the humidity, fullness of the tank, if ethanol is in the tank or not.
The water separator is doing its job. as fuel runs thru it, it separates the fuel and water--screw it off, empty, screw it back on, or change, depending on your beliefs. Then run the boat another XX hours and change it out again and see how much water there is. These filters do "wear out"--there is a water bloc in the elements, plus a certain amount of "damage" done by ethanol and just the fuel running thru, plus debris accumulating. I tend to change out the filter each time I take it off. Lets say every 100 hours or so--more often if high humidity, etc.
Now I just put some new fuel in my Caracal (140 Suzuki, 28 gallon plastic tank). I added appropriate amounts of Stabil, Sea Foam, Lucas top cyl oil and Startron. The fuel I put in had NO ethanol in it.
The fuel I was running earlier today was put in the boat 5 months ago, and was similarly treated.. Not run much between times, and ran like a top....