I had the same experience...
What I did was accidentally selected some post-fitting signals during my signal tap setup. I immediately realized this because those post-fitting signals were blue..I removed them and hope that it would still compile because I haven't save my design or anything..However, the compiler failed because of this "incremental compilation is not supported for web license"...Anyway...The GUI showed that incremental compilation is disabled and gray out, so I can't change anything....Then I opened up the .qsf file and found the following statement
# start DESIGN_PARTITION(Top)
# ---------------------------
# Incremental Compilation Assignments
# ===================================
set_instance_assignment -name PARTITION_HIERARCHY root_partition -to | -section_id Top
set_global_assignment -name PARTITION_NETLIST_TYPE POST_FIT -section_id Top
set_global_assignment -name PARTITION_COLOR 16764057 -section_id Top
set_global_assignment -name PARTITION_FITTER_PRESERVATION_LEVEL PLACEMENT -section_id Top
# end DESIGN_PARTITION(Top)
# -------------------------
By removing these statements, compiler is ever happy again
Is this a bug or Altera is trying to trick people to buy the full license?