Boro topped the Championship table in early November and remained in third place heading into the new year, yet just three wins in 2013 saw them finish the season down in 16th place - just five points off the drop zone.
Wednesday dominated against a poor Middlesbrough side at Hillsborough and quickly made their intentions clear as they secured Championship survival.
The Owls were in front in the ninth minute courtesy of Steve Howard before Leroy Lita added a second just after the half-hour mark.
Mowbray said: "They played how we expected them to play - they didn't have to work too hard for the first goal, it was self-inflicted.
"The second one, another set-play we conceded."
Of the season, while bemoaning an extensive injury list, he added: "Disappointing for us: we could have gone top New Year's Day if we'd beaten Derby.
"So for 27 games we were as good as anybody in this league, for the rest we have struggled, we've won three of them so it should be no surprise to us we didn't get a victory here, we have to get stronger I think.
"Ultimately the squad has to be stronger and deeper and try and sustain it.
"And hopefully you keep your best 11, 12, 13 players fit for most of the season but we've fallen away, we can't hide that fact, it is what it is."
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- Leroy Lita