It was not like the butcher hadn't dealt with Mana Bodies before.
The summoned creatures conjured by his opponents in the past could also defend themselves against Eren's physical attacks in a similar fashion.
However, the summoned creatures were limited by their intelligence. Plus, they were not able to control the flow of the mana within their bodies, making them vulnerable to Elemental Attacks. Especially if the attacks were of opposite elements than the elemental mana the Mana Body was made from.
Eren was used to deal with Mana Bodies by changing the elemental spells. For example, he would use water-element spells to deal with fire-element creatures summoned by his opponents and that would be enough to deal with them. He would use fire-element spells against woodland creatures, dealing with them effectively by taking advantage of their natural vulnerability against certain elemental forces.
