Mat Harrold left Devon earlier with a cut eye, and Benji van den Broek was injured in Town's first game.
Shrews boss Graham Turner told officials he "wasn't prepared to take chances with two games in two days".
Earlier in the week Turner had been in dispute with the Cup organisers over the number of substitutes allowed in games.
He was told sides could field only three but claims he had been previously informed they would be allowed five.
The Shrews beat Ilfracombe 5-1 and Rushden 1-0 in their group games to qualify for the semis, Blackpool beat Leyton Orient 2-1 in the other semi-final.
Shrewsbury are now preparing home friendly with Championship side Coventry on 27 July 27.
Source: BBC Sport
Source: BBC Sport