Another thing i came upon today, which happens to have an easy fix, is this:
When you upgraded your ports, and some option got changed, you will probably get:
doesn’t install the Apache module anymore: update your OPTIONS and build www/mod_php5 port instead
Now, since you already upgraded the ports tree, the option that you should uncheck and reconfigure the port is already gone, so you can’t fix it like that.
What you can do, is remove and reconfigure ports options, in my case being the php5-extensions
What i did was:
You will be prompted to reconfigure the options, and your upgrading will work just fine