I don’t know if this can be classed as a common mistake

Question

…but I’ve just realised why I get confused about when to use the subjunctive after ‘no sé que…’ (‘I don’t know that…’) or ‘no sé qué…’ (‘I don’t know which/what…’), now I realise that I should use the subjunctive in the first case and not in the second. Thank you!

Answer

Hola Ben
Just a little explanation on "(no) saber que + subjunctive" as it sounds from your comment that you're completely discarding the use of the indicative when you use no saber que...
You can use both, the subjunctive and the indicative in this case. The use of the indicative is going to convey a "declaration" of what the speaker "knows" or "doesn't know":

Yo no sabía que Marta tenía novio.
I didn't know that Marta had a boyfriend.
Nosotros sabemos que Marta tiene novio. 
We know that Marta has a boyfriend.

Both in the affirmative (sé que... sabía que...) and the negative (no sabía que...) the indicative can be used so the speaker somehow declares this as a fact and reiterates what they know/don't know. It denotes more "commitment" to the truth from the speaker. 
On the other hand, if the speaker doesn't want to show that "commitment" with what it's being said, they may use the subjunctive:

Yo no sabía que Marta tuviera novio. 
I didn't know that Marta had a boyfriend. (and I am somehow doubting this... not completely sure...)

I hope this is helpful.
Saludos
Inma