Your scientists did give the T-rex bigger arms, but they turned out to be an extreme danger during transport.
When soldiers strapped down the animal for transport, it was considerably harder to do with the extra large arms. These arms inevitably escaped or broke the restraints and several soldiers were killed trying to re-restrain the arms. These larger arms were also able to reach the harnesses for the head and legs, so were able to break these restraints as well. Three Chinooks, two C-130's, and even one LCAC were lost (in separate training accidents) due to the animals being able to get free.
The regular arm size was plenty strong, but small enough to be easily secured during transport. The smaller arms were also unable to reach any of the other restraining harnesses. The animals were also somewhat more docile with the smaller arms.
The larger arms seemed to confuse the animals, flailing them wildly around at times, causing harm to other animals, themselves, people, equipment, and buildings. Some animals even ended up dying after they chewed off their own limbs, or as much as they could reach. Since the animals wouldn't let anyone approach to tend to the wounds, they simply bled out. In the cases where they did this within a herd, the injured T-rex would end up getting attacked and eaten by the other animals, even before they died. This would sometimes end in a "feeding frenzy", where multiple animals ended up dead.
The scientists aren't sure if this was because of the presence of blood or because they would thrash around, injuring and angering the other animals.
Even when the animals survived to adulthood, went through training, and made it to deployment, they often turned against the soldiers releasing them from the restraints. The smaller armed animals needed less restraining, so were less likely to turn on their captors.
Due to the large armed animals' tendency to escape or turn on the people who released them, the idea of dropping the animals into a hostile area on it's own was considered. Unfortunately, all attempts to implement this ended in failure. Either the animal died on the impact of landing, were so dazed after landing they couldn't escape the container, or they attacked the container instead of the OPFOR. Even when the animal wasn't killed on landing, they were killed shortly afterwards with few enemy casualties.
With the extreme cost and low probability of being able to use these modified animals effectively in combat, a review board was convened. Further research was cancelled due to the unacceptable injuries, loss of life, and loss of material involved.