NO way that is 'normal'; your dealer is stroking you and is full of cowpoo. DO NOT continue to run that engine with the crap fuel in your tank!:talktothehand:
Get them to completely drain the tank as already stated until there is NO evidence of water in the tank and then flush the tank with fresh clean diesel and replace ALL filtration on the tractor. Then run it and verify the fuel/water separator is NOT still picking up water. If it is, there is still a problem. Clean and verify. Keep doing it until NO EVIDENCE of water is present. That is why you have a fuel water separator to begin with.
Diesel injection pumps are assembled in clean rooms with negative air pressure to make absolutely sure there are NO contaminants, including dust present during assembly. There are youtube videos showing the assembly process. Diesel systems that run on high pressure and microscopic size particles of fuel atomized for optimum combustion do not tolerate water or any other debris.
Solve it now or forever own the issues of a damaged fuel injection system. Trust me, you do NOT want to face the later option. Its ugly and wicked expensive.
We dealt with diesel autos in my foreign auto repair facility all the time, way back in the 1980's and then the fuel was loaded with sulfur and other lubricants not present today. Fuel must be atomized to combust as designed and water is not part of that equation. We used what Mercedes approved as the ONLY additive at the time- Red Line diesel fuel catalyst, which broke down water particles into smaller molecules to allow whatever minute quantities were present in gelled fuel filters to burn completely during combustion. We also replaced injectors that had wonky spray patterns and diesel injection pumps at thousands of $$$$ when they had been destroyed by contaminated fuel over time and lack of proper timely fuel filter maintenance intervals.
Do not take no for an answer from your dealer. Sit down with him and explain what is an acceptable result from your perspective and what exactly you expect him to do to fix the problem. Bring a witness to the conversation, and agree with him to the plan you outline for him to solve at his expense and time.
I'd want him to show several clocked hours on your hour meter AFTER he has done what I outlined as to tank drain and flush and all new filters, before you receive the tractor back from his shop. Record before service and after service hours on the meter on you phone camera with a date/time stamp for proof of your requirements of his work on your machine. Good luck; be nice about your requirements, but make it clear the it's 'normal' BS is NOT going to fly.:thumbsup: