Auto leading can be a convenient feature if the automatically selected leading amount works for your selected typeface. Generally, the software has a default setting that sets leading at around 120% or so of the type size. 12 point type would have 14.4 point leading, for example. In some programs you can change the default auto leading percentage.
Where auto leading can create problems is when you change the type size of just a portion of text in a paragraph. The software will automatically reset the leading for that entire line of text to whatever the auto leading specifies for that type size you just changed. This can result in paragraphs with some lines of text closer or further apart than others in the same paragraph. The fix for this condition is to set the leading for that paragraph to a fixed amount, even if that amount is the same as the auto leading for the bulk of the text.
Use auto leading when you haven't settled on a final font or type size for your document. However, once you've finalized your font and type size, go through and reset the leading in your document — even if that is the same number as your auto leading. This will prevent the leading from appearing differently when you share digital documents with someone who has a different auto leading setting for their software. Also, if you find that you need to change the type size of just a few parts of your documents you won't need to make manual adjustments due to the auto leading kicking in.
For a more detailed look at leading and auto leading: