Reformating code does not work properly

Since I have many (bad coded/indented) files, that look like this:

After doing a reformat, most code is indented right, but some parts still look like this:

After having a closer look (with sublime) I noticed, that these lines are not indentet with tabs, but with spaces:

So why are those parts not indented right with tabs?

Additional question: How can I remove the empty lines for the hole project?

Thank you!