I've attempted to reproduce the issues you're experiencing and cannot do so. What browser (and its version) are you using the online release with? Could we get a look at one of the "good" files that you're attempting to import?
Also. An actual line break, and/or tab, in the exact spot shown in your example will not cause an error. Neither SugarCube, nor JavaScript, would have issue with regular whitespace in the area depicted, nor would they care what it happened to be, line breaks and tabs included.
If you are receiving an error from the exact construct shown in your example, then it cannot simply be line breaks and/or tabs alone that are being inserted. For example, the following is perfectly valid:
<<set
$myVar
to
"No errors here."
>>
Could we get the actual error message?