The title of the thread doesn't quite correspond to the OP. I presume that this was a spin-off from a discussion on a different thread.
We can all speculate as to what Pinto actually meant, but it's not entirely clear.
I can think of a few potential ones, but obviously only IMO.
- In view of the fact that there was a torture investigation concerning a certain other missing child case involving several of the officers in this case, it might have been better to quietly put them on gardening leave (or assign them to something totally different) and draft in a different team. Whether that would have been feasible or not... no idea.
- Forensics: it wasn't thoroughly done (this isn't a criticism of the individuals themselves, as I have no doubt that they did their best with the resources and training at hand).
- Potentially useful CCTV footage in PdL wasn't secured in time (namely the camera near where the Smiths were staying). Whether he was head honcho or an office boy, Amaral was the coordinator. How many CCTV cameras could there have been at the time? It's not like it was a sprawling metropolis.
- PJ leaks.... Vast subject.
- Possibly not initially embracing support from the UK. The other side of that coin is that the UK may have made the PJ team feel that they were being swamped.
I expect that I could think of a few others, but I'm not suggesting that it was all bad, either.
In relative terms, I can think of a different missing child case that I find jaw-droppingly more worthy of "I’m convinced the XX case will feature in Portuguese judicial history as a bad example. What a criminal investigation should not be."
ETA: and my last point is related to the first.