There's nothing wrong with your sentence. The submission of something need not be an immediate event.
For instance, submitting an application for a passport could take a long time, if you need to track down a whole bunch of documents, get a passport photo, and then mail it or travel to a government office.
The act of submission can refer to the extended process rather than to the final act at the conclusion of the process.
In your example, let's say the following:
- I'm an artist and I've approached the curator of an exhibition about having one of my sculptures displayed.
- I haven't finished the piece, but I've got a picture of its partial progress.
- I'm also famous for similar artwork in the past, so the curator is fine with it not yet being finished.
At this point, I can be considered to be in the process of submitting my sculpture to the art gallery. It's just that I haven't finished it yet, so it will take a few more weeks.
- For whatever reason, I keep the unfinished sculpture in a closet when I'm not working on it.
- One morning, I open the closet door to keep working on the sculpture and discover that it's missing.
- I assume somebody must have stolen it, so I call the police.
- A police officer comes to my house and starts writing up a report on what happened.
The police officer says this to me:
"So, let me get this straight. The sculpture that you were submitting was in that closet. But it's not there now?"
In terms of the actual background for the sentence that you gave in the question, while there is nothing ungrammatical about the sentence, it doesn't actually describe the situation.
In the actual background, you say that the remaining pieces were in the closet. Given that, the sentence used should have been something like:
Those pieces for the sculpture that you were submitting were in that closet (all along).
As a last note, you can say this:
I was breaking the window while playing catch ball.
You have two hands (and two feet). It's theoretically possible to do both at things at the same time. Especially if breaking the window isn't a simple process. (Nor would it be, if you were playing catch ball at the same time.)
Just because it's unlikely from a practical standpoint, that doesn't mean it's impossible—or that the grammar is wrong.