The thing that comes to mind is Gajeel's earlier portrayal. In the manga, his initial antagonism toward Levy and the others is harsher, with more graphic panels showing the Phantom Lord guild's attack. The anime softened that a bit, maybe for broadcast timeslots. They also extended some of the comedic filler moments, like Lucy's apartment antics, which sometimes made the characters feel slightly more slapstick than Hiro Mashima's art.
I've noticed the anime gives more breathing room to side characters like the Exceeds earlier on, but at the cost of diluting the urgency of certain arcs. The biggest shift for me was in the Tartaros arc. The manga's depiction of character deaths, like Makarov's apparent sacrifice, felt more definitive and heavy. The anime's adaptation trimmed some of the darker imagery, altering the emotional weight. It's a common shonen adaptation issue, but it changes how you perceive the stakes.
Gray's development around his father also seemed more rushed on screen, blending moments that were distinct in print.