The sentence, exactly as it's written, is ungrammatical.
There are two possible ways of interpreting the meaning—and it's not possible to know what was intended without more context.
1. Parenthetical Nonessential Information
If the information between the comma pairs is meant to be nonessential, then removing it and the commas should result in a grammatical sentence.
In order to for this to happen, make needs to be changed to makes:
The confusing unmatched bracket, and the fact that it is a fragment rather than a whole sentence, makes this hard to evaluate.
This could also be rephrased to put the nonessential information at the end of the sentence:
The confusing unmatched bracket makes this hard to evaluate, as does the fact that it is a fragment rather than a whole sentence.
2. Essential Information
If the information between the comma pairs is meant to be essential, then the commas need to be removed:
The confusing unmatched bracket and the fact that it is a fragment rather than a whole sentence make this hard to evaluate.
This could also be rephrased to make the conjunction of the two terms more obvious:
This is hard to evaluate because of the confusing unmatched bracket and the fact that it is a fragment rather than a whole sentence.