There is plenty that went wrong, so much so that it took a miraculous September run for the club to have any shot at a playoff spot. For much of the season injuries and underperformance caused serious problems. Heading into the season this looked to be one of the most talented and complete Jays rosters in recent memory, but despite that this club floundered through much of the season.
You can basically look at this season as two separate parts, there are the first 5 months of the season where the team was only a few games above the .500 mark for the most part, and September where they caught fire and look like the best team in baseball. Prior to the trade deadline in particular the club had a ton of issues that led to a lot of lost games.
For the longest period of time they received basically nothing out of the third base position. People seem to want to argue that Biggio being hurt most of the season is insignificant, but heading into 2021 he had almost been a 4 win player in his first full season's worth of games. Receiving a sub replacement performance out of a player like this is not a small deal. Espinal ended up stepping up for a period, but then he ended up getting hurt as well. Panik was played by the manager almost every day despite being sub replacement.
Biggio's lost season and Tellez's lack of production ended leading to the team having no good left handed options in the lineup. The club has a lot of very good/elite right handed hitters, but a little more balance in the lineup would have likely helped the team receive a little more offence against the parade of righty relievers that the opposition has been able to shut down the Jays late in games for most of the season.
For the start of the season the club received very little out of the catcher's position, and when Kirk came up and started playing well he ended up injured and missed a good chunk of time as well. Jansen missed a bunch of time on the injured list also, although that may actually end up being a blessing in disguise as he may have turned things around a bit during his AAA stint.
For the first two months of the season Gurriel looked like one of baseball's worst players, and was still at replacement level at the start of August. It has taken a remarkable hot streak for him to start looking like a player who was actually worth rostering.
The rotation has also had it's share of issues. Roark was given a roster spot and ended up being cut from the roster. Pearson ended up with a chronic injury and missed another year of development necessitating trading for Berrios. Ryu has looked to hit the decline phase of his career in a serious way, Stripling started the season looking completely lost, finally found it but then ended up missing time due to injury. The rotation has ultimately ended up as somewhat of a surprise strength as the season went on but this wasn't the case early on in the season in particular, when the club received terrible performances from the likes of Roark, Zeuch and Kay.
It's impossible to gloss over how much of an issue the bullpen was in the first half of the season prior to the additions of Cimber and Richards. If the team ultimately ends up missing the playoffs this is going to be the major reason given how many leads were coughed up earlier in the season.