The Blues led after dominating much of the first half.
Layton Watts, recalled to the side, broke the deadlock, on 21 minutes.
However, Merseyside hosts Prescot Cables promptly levelled on 69 minutes and stunned the Blues with a second goal within six minutes.
They held on with an injury to goalkeeper Shane Bland marring a day to forget for the visitors.
Whitby Town TV spoke to Watts after the final whistle, he thought missed chances made all the difference:
" Disappointed first half, so comfortable, obviously. Probably should have took more [chances]. Our chances could have been three easily, and then second half, it's a total different game, I think. Obviously, they've put a lot of pressure on us, but we just haven't answered back with anything. We've just sat down and let them do it, so really frustrated. One for us to take, yeah, three points missed out on, I think."


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