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This answer suggests that commas should always be put before dass. However, what about this sentence here?
Ich dachte es war einfach für dich, nicht dass du Probleme hattest.
It seems to be that it would be a bit strange to put a comma before the dass here. (Sorry for any grammatical mistakes in the sentence – I made it up)
There is a comma before dass very often, but not always. You can even find counter examples in the official spelling rules, §72, like this:
Ich hoffe, dass es dir gefällt und dass du zufrieden bist.
This is probably the most common case in which the general rule that you are referring to in your question does not apply: two subclauses linked with a conjunction like und. You can find a short discussion of more cases in this (German) blog post by "Dr. Bopp".
Regarding the sentence in your question: there is a comma missing behind dachte. But I would rather not put a comma after nicht. It is not a clear unambiguous case, and I surely see a point in this answer. However, I am reading the sentence the way that there is intentionally no und before nicht. The two subclauses are meant to be contrasted, not joined or simply enumerated. If there is a missing a left-out conjunction at all, it is aber, not und.
I did think it was easy for you. (But) I did not think that you had problems.
When nicht is used as a contrastive negation word, it is placed before the part of the sentence it emphasizes (Source: canoo.net). Hence I think that nicht belongs to and starts the second subclause, and that we have a multi-part subclause introduction like it is handled by §74 E1 of the official rules:
E1: Besteht die Einleitung eines Nebensatzes aus einem Einleitewort und weiteren Wörtern, so gilt:
E1.1: Man setzt das Komma vor die ganze Wortgruppe.
You might also want to compare your sentence with this one, which is also from the official rules (§71):
Dass sie ihn nicht nur übersah, sondern dass sie auch noch mit anderen flirtete, kränkte ihn sehr.
Reversing its meaning, but keeping the structure, we could write
Dass sie ihn übersah, nicht dass sie auch noch mit anderen flirtete, kränkte ihn sehr.
Finally, there is a passage in "Duden Ratgeber - Handbuch Zeichensetzung" that reads
Mit einigen Konjunktionen oder Adverbien bildet "dass" Fügungen, die in der Regel als Einheit empfunden und meist nicht durch Komma geteilt werden. Das Komma steht also nicht vor "dass", sondern vor der ganzen Fügung:
...
Ich wusste von Deinem Brief, aber nicht dass du kommst.
Lets start with the contained two sentences in raw form:
Ich dachte, es war einfach für dich. (1)
Ich dachte nicht, dass du Probleme hattest.
Now we can combine them
Ich dachte, es war einfach für dich, und (ich dachte) nicht, dass du Probleme hattest.
Omitting und in the resulting sentence is something done in oral language but discouraged in writing, since it is inferior style. The und joins the two sentences, but does not influence the comma rule in question here. Let's use a semicolon instead, just for fun:
Icht dachte, dass es einfach für dich war; nicht, dass du Probleme hattest.
Note (1) Since the second sentence tells us that the first sentence is an assumption that has not become true, and thus remained a mere possibility, it might be beneficial to employ a conjunctive form here:
Ich dachte, es wäre einfach für dich.
Or, using dass:
Ich dache, dass es einfach für dich wäre.
You may also use conjunctive form in the second sentence to accomodate for the one in the first sentence:
Ich dachte, dass es einfach für dich wäre; nicht, dass du Probleme hättest.
This is probably closest to what you would be hearing in a normal conversation, although people tend to use the perfect tenses instead of past tense, like:
Ich hätte gedacht, dass es einfach für dich wäre; nicht, dass du Probleme (gehabt) hättest.
If we put that sentence into a non shortcutted version you'll see it much better: Ich dachte, es war einfach für dich und nicht, dass du Probleme hattest. Whenever encountering sentences that make you question the rules, check if your sentence is well formed.
Now you should also see that we have two combined sentences: Ich dachte, es war einfach für dich. Nicht, dass du Probleme hattest. Two sentences are best combined with a semicolon.
