Files missing when installing from ports after upgrade to FreeBSD 11

So I recently upgraded my system to FreeBSD 11, and when recompiling packages I noticed that some files are missing (and it is always the same files).

For example, when installing perl5-5.24.1.r4, it installed perl binary but perl5 and perl5.24.1 were missing.

When installing bind99, /usr/local/sbin/named was missing.

When I perform "make package" and then install the resulting package then all files are installed as they should.

I did not have this issue when I was using FreeBSD 10, was there any change that could cause this?

Edit: More info, the files do exist in stage directory after "make stage", and it's possible that missing files are hardlinks.
Did you delete and reinstall all packages? If you installed new ports after a major version upgrade, that does not work. Either never touch the installed ports after that type of upgrade, or delete them all, then reinstall. There is a procedure at the end of the ports-mgmt/portmaster man page. pkg(8) does this automatically, I think.
Yes I reinstalled all ports ( portmaster -af), the issue is happening every time I reinstall affected port.