The principal [problem] with these programs [are] conflicting codes.
The principal [problem] with these programs [is] conflicting codes.
Note: In sentences like this one, in which the subject (principal problem) is singular and its complement (conflicting codes) is plural, the verb agrees with the subject.
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See Error Checklist for a compilation of 75 common writing errors.
For more exercises in identifying common errors,
take the M.B.A. exam and the Punctuation and Grammar Challenges.