They later said the only finished animations were the ones in the trailer. Live action filming was done, but they had barely gotten started on the CG animation when the awful trailer dropped, so it was easy to change course and redesign Sonic for the rest of the film. Also, the film was delayed while they made changes, so it did cause a setback.
Although I would believe that somebody dropped that trailer to prove a point that no one would watch a Sonic movie with that abomination. After the outrage and public backlash, the point was proven and whomever greenlighted the original design backtracked and let the animators fix it.