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.
And Bologna helps a lot with your education, by making higher education comparable between EU countries, you can easily apply for student exchange programs and study subjects that aren't approached by your home university.
I studied in one of the best engineering university of Portugal and I studied for one semester in Sweden and although both universities were under the Bologna agreement, I could notice differences in both systems.
The only thing that Bologna imposes in universities is how many hours of effort is 1 course credit (ECTS). Course content, organization and etc, is up to each university.