As far as I know, Nelson Mandela did not ever accuse Israel of being an apartheid state, nor make a comparison of it to apartheid. While his relations with Israel were never overly friendly, and he always had clear personal inclinations towards the Palestinian side, Mandela was also clear quite frequently that Israel had a right to exist. He was also quite clear that Zionism, the movement for the establishment of a Jewish state, had to be recognized as a legitimate national movement the same way he recognized the Palestinian desire for a state as a legitimate national movement.

Mandela certainly drew comparisons between the ANC and the PLO, but never in the context of being anti-apartheid movements. Instead, he made comparisons about the desire for self-determination between the two, and the need for Palestinians to experience statehood and freedom. He rarely seemed to lay blame at the feet of Israel exclusively for this, but as I mentioned, he also was not always friendly with Israel. I'm not familiar with any warning of potential apartheid later as well. It's hard to prove a negative, but I don't believe there's an indication that Mandela believed Israel was or might become an apartheid state; typically, the sources claiming otherwise are referring to the Fassed letter, which has gained purchase in many circles today. It was even cited by President Carter.

Fassed claimed the memo was never meant to be taken seriously. He claimed people had forwarded it along without including his name, which is why it got confused, though that's unclear. I'm not sure Mandela ever spoke about it; if he did, I can't find it. I have always found that strange, but frankly, maybe it simply never crossed his radar; the letter's popularization came when he was well past 80, and he may simply have never seen it or felt the need to respond. His health was a struggle by 85, and it only really started to spread nearer to 2007, when he was almost 88. Perhaps, as I said, he simply never saw it or was unavailable to really talk about it, by that point.