You can for a certain script/css file set the maximum level compression to ever be used for it. For example you might have found that from all your 100 js files there is one file - foobar.js which doesn't work when packed. But it does work when whitespace removed.
You can still use IncludeScriptsCompression=2 (I do recommend it as a matter of fact) - but you can then override the maxlevel for that specific file:
<headermanager:IncludeScript Path="~/scripts/foobar.js" HighestCompressionLevel="1" />
now all files will be packed level 2 - except that file.
Or of course
<headermanager:IncludeScript Path="~/scripts/foobar.js" HighestCompressionLevel="0" />
will not touch the file at all.
There is also another way. Say you managed to (by hand) create a packed and obfuscated file for foobar.js. Jou call it foobar.pack.js and now you can use:
<headermanager:IncludeScript Path="~/scripts/foobar.js" StaticPathLevel2="~/scripts/foobar.pack.js" />
Which means that when level 2 packing is asked for - then a static URL to the foobar.pack.js will be used instead.