The "Show Non-printable Characters" feature displays a ¶ symbol (U+00B6) to indicate the end of file. Since it's the same symbol used for line feeds, it's confusing and makes it difficult to spot whether the file ends with a carriage return.
*** Bug 207508 has been marked as a duplicate of this bug. ***
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue.
Thanks for your cooperation,
NetBeans IDE 8.2 Release Boss
The issue still persists in latest development build available today (netbeans-trunk-nightly-201607100002-php-windows-x64.exe).