Yes. If there is water in the plug well and you remove the plug, the water drains into the cylinder. It's good practice to blow air into the plug well with the COP removed prior to changing the plug to keep any debris from entering the cylinder.
I've never had an issue with water. Water will evaporate quickly when the engine reaches operating temp. I cannot imagine a scenario where water was causing a consistent misfire unless you didn't have a hood and it rained every day. Oil, on the other hand, will cause the coil to short to the block under load. Motor oil does not play well with the coil's rubber insulation. I didn't have a CEL, but the misfire was obvious under load. And the dealer was able to identify the failing COP and replace it in short order.
Any decent Ford dealer can put your car on a rolling road and find the misfire under load. Non-decent Ford dealers exist that are incapable of diagnosing a misfire to a specific cylinder, but in my experience they are the minority, thankfully. The first Ford dealer I took my car to wanted to replace all the COPs because they couldn't find the issue. I paid them $90 for their asinine opinion and drove down the road to the next dealer who identified the issue and fixed it. ****ed about the first shop, happy to pay the second. Private shops and "non-decent" dealer shops won't have that level of equipment, forcing them to throw parts at the problem, costing you money and not solving the problem.
