Missing six regular starters from their successful FA Youth Cup campaign, the Pilgrims found the going tough in Nottingham.
On the plus side, goalkeeper Jamie Bradley made a welcome return from injury after an extended lay-off.
Boston (4-3-3): Jamie Bradley; Harry Bunce, Josh Spencer, Billy Hodgkiss (Joe Cain 55), Corey Newman; Miles Lynch, Louis Saebe, Jordan Sowerby; Leon Squire, Karolis Andriulionis (Liam Moran 60), Steven Dovey (Joe Pocklington 60).