While the current does essentially follow the coast line there are eddies and counter currents closer to shore and around obstacles like Faulkner Island. This is true even in the Hudson River which may have stronger currents then the LI Sound.
The other thing is a question about the track you uploaded. Should I assume it is from your GPS? We use our Garmin GPS during races and it saves many of our previous tracks. I'm wondering if this is where the leg you marked with a "?" came from. There are also moderate wind shifts that occur which would help explain the not so 'erratic' course you show.
I applaud your attempt at figuring out how this deviation may have happened as it may help you navigate more precisely in the future. It also may not as the conditions vary from day to day. One thing you can do is to monitor your GPS and heading to see when you are getting 'headed' and tack to the other point of sail.
"The cure for anything is salt water~ sweat, tears, or the sea." ~Isak Denesen
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