The Army could veto transports. What Wisliceny did not tell, and what is perhaps more interesting, is that the Army used its right of veto only in the initial years, when German troops were on the offensive; in 1944, when the deportations from Hungary clogged the lines of retreat for whole German armies in desperate flight, no vetoes were forthcoming.)
In other words, they allowed deportations of Jews to clog their lines rather than veto in order to use those lines to aid their retreat.