James Norwood’s double ensured Rovers remained in second in what could be a dress rehearsal for next month.
The two clubs met in last season’s play-offs and Waddock says errors cost them on Saturday, just like they did last May.
The boss told Shots TV: “We did very well until they scored and mistakes have cost us dear yet again.
“We had the same situation against Tranmere last season in the play-offs. We’ve come up here to a good side, an outstanding club, and we’ve got to put it to bed quickly.
“Ifs, buts and maybes - that’s been the story all season. We had a good chance in the first half and if we take that, the whole course of the game changes. Tranmere know how to win games, they are a good outfit.
“The target is to get three points on Tuesday (against Gateshead). We can’t look too far ahead and you have to move on very, very quickly.”
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