Magilton seemed to be headbutted by Peter Rojczi, but then retaliated by pushing the Hungarian which earnt both players a red card for their respective teams.
Dean Bowditch was on target again for Town in a match which he replaced Nicky Forster after 20 minutes through injury, Town's other goal came from midfielder Darren Currie.
Town's defence still looked the weak link however, and Town boss Joe Royle will be concerned at the three goals his side leaked in the game which ensured Town suffered their second pre-season defeat.
Young Irish midfielder Owen Garvan featured in the game from the start, and impressed as he pushes to be involved in the first league game of the season against Cardiff City.
Ipswich Town: Price, Wilnis, Richards, De Vos, Garvan, Naylor, Magilton, Forster (Bowditch, 20) Parkin, Currie and Westlake. Subs not used: Collins, Trotter, Casement, McDonald and Supple.