It's not a bug, it's just a conflict between Link2SD and Android's native app2sd method. To avoid that and enable link2sd autolink for all apps, in settings check "Autolink" of course and set the installation location for apps2sd method as "Internal". Here is the question from the Link2SD FAQ:
Q. Altough "auto link" is on, some apps are not linked to SD card
automatically, instead, I see that that they are installed on SD card
with native app2sd method of Android. I need to link them manually?
A. Beginning with Android 2.2, application developers can express the
preferred installation location for their applications in the manifest
of the apps. The attribute supports three values: "internalOnly",
"preferExternal", and "auto". At install time, the system checks the
value of android:installLocation and installs the application .apk
according to the preferred location, if possible. If the application
has requested external installation, the system installs it in the SD
card. If the attribute is "auto", the system will decide where to
install the application based on several factors.
If an application is installed on SD card with native app2sd method,
it can not be linked to SD card with Link2SD. You need to link it
If you decide to use Link2SD and "auto link" on, set default install
location to "internal" within Link2SD to prevent conflict Link2SD and
native app2sd. In that case, apps will be installed in internal
storage even if the application is declared as "preferExternal" or
"auto" and Link2SD can link its files.