So Barry goes back in time and puts back the can of tomatoes.
But that causes problems so he goes back in time again to remove the can of tomatoes again.
But wouldn’t his mom look at the cart at checkout and say what happened to the can of tomatoes and either goes back and gets it since it is required or someone in the store gets it for her.
Maybe that is what creates the new timeline where Batman is Clooney now
I don't think this is the kind of movie that you think about things too much.
Just enjoy Michael Keaton as Batman.
Nora forgot the can of tomatoes the first time and sent Henry to get it, so not noticing it wasn't in the shopping cart at check-out is something that already happened. In this instance even if Nora saw it in there after Flash put it in, after Barry took it out she may not have due to the interaction with Barry in the Grocery store, it likely distracted her mind, as I'm sure she felt he looked familiar to her (or at least something was odd).
What happening in that timeline to cause the tins of tomatoes to go from the middle shelf to top shelf so Henry had to reach up and his face be seen I don't know, didn't look like Barry rearranged them when he put the tin back on the shelf (unless he did after he left Nora).