LaTeX uses & to separate the cells/columns in table rows so `foo & bar & baz \\` is one row with three cells/columns with the text "foo", "bar" and "baz" respectively. That is perfectly normal. If these ampersands show up in your PDF something else is wrong somewhere. It is impossible to tell what it is without seeing your Markdown source for the whole table and the LaTeX Pandoc produces from it. Try to get a minimal working example (MWE) by copying the Markdown source for just the table into a file of its own and converting that to LaTeX and PDF. If the problem persists attach the input and output from the MWE to a message so we can have a look at it (obviously removing/replacing any sensitive content as long as it doesn't affect the result.)