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I thought this post from XLINT89 (Kevin) was so good that I would copy to here and lock it. Excellent (pun intented) starting points. 
There are a few things that can cause a particular piston to fail. Simply replacing the piston and not correcting the problem will result in another failure.
Possible causes:
Obstruction in the fuel lines - Prob not in your case since it's 1 piston in particular
Restrictor missing - if your fuel lines were ever replaced and the restrictor wasn't re-installed, then that can cause a fuel pressure drop. ESP in the PTO (rear) cylinder.
Adjustment on carb is wrong - If someone has ever messed with the carb adjustments, thay may have leaned that carb out too much.
Dirty carbs - may need rebuilt or thoroughly cleaned. There are filters inside the carbs that may be clogged.
Wrong spark plug - I know the BPR7ES is recommended, but most feel the BPR8ES is better. It's a little cooler spark and should be gapped at .028"
Timing off - if the timing is too advanced, it will cause a hole. Most likely not your issue as it will affect all 3 cyls.
Out of phase crank - if you ever flipped the ski and got water inside it then hit the start button, you may have hydrolocked it. What that means is the water won't compress inside the combustion chamber, so the crank or rod bends or gives and forces that cylinder out of time or phase. Very good chance this might be something for you to look into.
Air leak - You may have a faulty gasket seal somewhere allowing air to leak into the engine and lean out the fuel mixture. Common causes are crank seals, base gaskets, head gaskets, carb gaskets, intake manifold gaskets, or exhaust manifold gaskets. Another one for you to look into.
Oil system has nothing to do with a hole in the piston center.
If I were you:
Remove the autocock if it's still installed on your ski, per the Polaris service bulletin.
First check your carb adjustmets to the specs in the manual
Rebuild the fuel system. Carb rebuild kits, new fuel hoses, new fuel filters, clean/replace the fuel selector valve, and install the triple outlet fuel pump.
Perform a leak down test. Looking for an air leak. There's a procedure for this test.
Index your crank. There's also a procedure for this as well.
One of these will help locate the source of your problem, and fix it for good.
There are a few things that can cause a particular piston to fail. Simply replacing the piston and not correcting the problem will result in another failure.
Possible causes:
Obstruction in the fuel lines - Prob not in your case since it's 1 piston in particular
Restrictor missing - if your fuel lines were ever replaced and the restrictor wasn't re-installed, then that can cause a fuel pressure drop. ESP in the PTO (rear) cylinder.
Adjustment on carb is wrong - If someone has ever messed with the carb adjustments, thay may have leaned that carb out too much.
Dirty carbs - may need rebuilt or thoroughly cleaned. There are filters inside the carbs that may be clogged.
Wrong spark plug - I know the BPR7ES is recommended, but most feel the BPR8ES is better. It's a little cooler spark and should be gapped at .028"
Timing off - if the timing is too advanced, it will cause a hole. Most likely not your issue as it will affect all 3 cyls.
Out of phase crank - if you ever flipped the ski and got water inside it then hit the start button, you may have hydrolocked it. What that means is the water won't compress inside the combustion chamber, so the crank or rod bends or gives and forces that cylinder out of time or phase. Very good chance this might be something for you to look into.
Air leak - You may have a faulty gasket seal somewhere allowing air to leak into the engine and lean out the fuel mixture. Common causes are crank seals, base gaskets, head gaskets, carb gaskets, intake manifold gaskets, or exhaust manifold gaskets. Another one for you to look into.
Oil system has nothing to do with a hole in the piston center.
If I were you:
Remove the autocock if it's still installed on your ski, per the Polaris service bulletin.
First check your carb adjustmets to the specs in the manual
Rebuild the fuel system. Carb rebuild kits, new fuel hoses, new fuel filters, clean/replace the fuel selector valve, and install the triple outlet fuel pump.
Perform a leak down test. Looking for an air leak. There's a procedure for this test.
Index your crank. There's also a procedure for this as well.
One of these will help locate the source of your problem, and fix it for good.
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