Is it bad to submit applications for two different degree programs in the same department of a same university?
Based on the tag, I will give a US-specific answer.
Often, but not always, the difference between the masters and the first part of a PhD is that the PhD program comes with funding.
If your intent is to get the PhD eventually anyway, I would not recommend considering an unfunded masters.  This is essentially the same as starting a PhD without funding.  Reasons not to do that are discussed in Is it worth self-funding a PhD to attend a top 10 university?.