Before the Bologna process, engineering and CS degrees in Portugal used to be 5 year courses, minimum. After the Bologna process, curricula were modified so that courses could have a 3 year minimum.
This, by itself, isn't a bad thing.
However, the market perception is that these 3 year courses give the same level of qualification as the previous 5 year courses. It doesn't help that the name of the degree has been made the same on purpose ("licenciatura"). "They just removed useless stuff," they say.
This feeds back into students as "no need to go any further." Once they have reached the degree that the market recognizes (the "licenciatura") there isn't much incentive to continue for another 2 years to get a masters degree (btw, in the previous system a masters degree was 7 years).
Universities have to handle this somehow, and they do it by actually "removing useless stuff" from the 3 year curriculum thus reinforcing market perception and actually putting themselves on course to become training schools instead of universities.
These arguments are pretty specific to the portuguese case, and elsewhere things are bound to have been different but with the same general outcome. The general argument is this: solving the comparability problem between EU countries went too far and breached the universities' ability to resist outside influence (mainly political).
PS: The ECTS system is deeply flawed exactly because it is based on "hours of effort." Not only bacause that's a subjective measure on its own, but mainly because "effort" does not directly correlate to actual learning. A course may have very work-intensive assignments for very little knowledge.