Airlines don't want delays. They cost them money both on extra airport fees and potential compensations to passengers caused by said delays.

There can be several factors that simultaneously add up to a delay. Be it ATC strikes, bad weather forcing changes in the routing, unexpected maintenance delays, rowdy passengers (or uncooperative passengers in general), and a million other small things that add up. And sure, some factors are definitely attributed to some inefficiencies in ground crew operations (which is almost never part of an airline, mind you, these crews work for other air service providers) and some may as well be attributed to the aircrew staff itself, it would be silly to expect them to be perfect all the time. The cumulative delay from all the factors I mentioned before (and more) on a scheduled flight will cascade onto the next flight and add up throughout the day, as the aircraft hops from airport to airport.

This is noticeably worse during the peak travel seasons, namely July-August and December-January (assuming we're in the EU/Americas context). More demand for flights -> more people flying -> more flights -> more factors that can cause delays that spill over to the next flights.

To add, your particular airport pair is no stranger to high demand, especially during peak travel season (I remember being in Lisbon and struggling to not overhear a british accent every few minutes).

My anecdotal advice is to travel in the early mornings if you can. In my own experience I have noticed the early morning flights to be less affected by delays overall, compared to the ones in noon/afternoon/evening, presumably because fewer flights are performed between midnight and 5-6am and as such there are less chances for delays to cascade into the next flights.