Transpose a progression and some chords may come out spelled in a way you would not have chosen, especially in a song that modulates. iReal Pro picks its spellings by counting from the song's original key, which reads well for a song that stays in one key and imperfectly for one that does not.
The problem is genuinely hard rather than neglected. Deciding where one key center ends and the next begins is difficult to do reliably, and players disagree about whether they would rather see a B# or a Cb. It stays on our list.
To fix a song by hand, duplicate it, use Set and Transpose in the Editor to move it to the key you want, correct the chord symbols that bother you, and save. This sits awkwardly with a transposing instrument, since the chart you corrected is transposed again for your instrument.
For the full guide, see Transpose a song on the iReal Pro website.