Even if the post was written back in 2016, I've seen this
Dotfuscator CE Build Error: External type not found System.Windows.Input.ICommand,PresentationCore - Stack Overflow[
^] which worked for me.
You will have to:
1 - find your dependency assembly path in your system
2 - manually add it to your DotfuscatorConfig.xml file under a section <loadpaths> or use the DotfuscatorCLI program to add the assembly path (as the referred post on StackOverflow's answer suggests)
3 - try to compile again
4 - celebrate the success or face the next unresolved assembly dependency (go back to 1)
Hope this helps to whomever in the same or a similar situation.