The Pilgrims had four under-16s players on the pitch by the end of the match at RAF College Cranwell and were beaten courtesy of 18th and 25th minute strikes from the visitors.
The result left United searching for their first league win of the season — but with key players rested ahead of Friday’s League Cup third round tie against Birmingham City.
Boston (4-4-2): Sam Vince; Daniel Worthington, Niall Delahoy (Todd Devlin 62), Charlie Melville, Corey Newman; Miles Lynch, Jordan Sowerby, Lewis McKue, George Stainfield; Juris Kormis (Karolis Andriuilionis 66), Leon Squire (Joe Cain 62).