Rikky Barnes scored with a tap-in for Mere, but Crewe succeeded from two short corners to take maximum points.
The result leaves Windermere in sixth place, four points behind leaders Wilmslow.
Mere’s man-of-the-match was fast improving 15-year-old Ed Brownell.
By contrast, Windermere seconds beat Blackburn seconds 5-0 to climb to fourth in North West League Division Five North.
Aidan McDougall and Luke Blezard, with a penalty stroke, gave Mere a 2-0 half-time lead.
Tom Whitehead and Ed Evans added two more before McDougall beat the keeper in a one-on-one situation to complete the scoring.
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