The trio missed the home draw with Swindon last weekend. Hodson and Carruthers were away on international duty with Northern Ireland and the Republic of Ireland Under-21 side respectively, while Flanagan was nursing an ankle injury.
All three players face competition if they are to force their way back into manager Karl Robinson's starting XI. In Hodson's absence, Jon Otsemobor has performed well at right-back while loan duo Jason Banton and Danny Green have impressed on the wings.
Daniel Powell (ankle) and Dean Bowditch (groin) remain sidelined through injury. The latter returned to training this week while Powell is still in the early stages of his rehabilitation.
MK Dons last week