As always, each case turns on the facts.He was fired for 'lack of candor' with investigators and false statements. Isn't that the same crime they have Roger stone and Flynn for ?
The DoJ may have seen that the case against McCabe was weak, if they had a case at all. Lacking candour may not be professional if it happened at all, but may not be a prosecutable crime. It went to the grand jury and they didn't indict, probably through lack of anything to prosecute, and apparently one of the prosecutors themselves had doubts about the merits of the case.
Whereas the case against Stone was likely more credible.
And let's not forget the run up to McCabe's firing. Trump had a bee in his bonnet about McCabe and was pressuring those he could to get him fired and was gleeful when this eventually happened.