Here are the broken recipes I've encountered so far (some already mentioned):
--Unburnt clay brick. It's asking for Angel's Refining Clay, whereas the Pyanodons HighTech Clay is the only type of clay available.
--Simple circuit board. There are now two recipes available, a more difficult version of the old recipe inside a Chipshooter Machine that adds solder as an input, and a much easier recipe that just needs Copper plate, Copper cable, and Wood. The easy version lists no machine requirement, so I believe an assembler should process it, but there is no option in the assembler recipe menu. You can hand-craft the easy version, but can't automate it since you can't make through an assembler.
--Basic electronic components, from Angel's Industries. There is no recipe for this item that I can find. This breaks Logistics/Construction Robot Brain 1, as an example.
--Transistors, from Angel's Industries. There is no recipe for this item that I can find. This breaks Logistics/Construction Robot Brain 1, as an example. There is a separate Transistors item from Pyanodons HighTech, but it is not interchangeable.
Among these, the clay brick bug is a huge progress blocker. Clay bricks are needed for many early game machines like the Electrolyzer.