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I've come across it in the 12th episode of the 3rd season of the Walking Dead. Here is the context:
Morgan: You will be torn apart by teeth or bullets.
You and your boy.
Your people, but not me.
Because I am not gonna watch that happen again.
Man, you take the guns.
Rick: You know there's a chance. That's what you can't square.
In this context, "square" means "balance", or "settle" or "agree".
https://www.merriam-webster.com/dictionary/square
The usage is a little odd, but good synonyms in this sentence would be either "accept" or "justify".
5 a : exactly adjusted : precisely constructed or aligned (MW)
To “square” things in construction is to align them, to make them fit together correctly.
We can apply the same meaning to ideas, meaning to make two ideas fit together in our minds. This is usually in the form “can’t square X with Y”, but in your example, both X and Y are presumably supplied by context. (One of them seems to be having guns, but I can’t find the other in your quote.)
