Yes, comics storylines are weird that way. I remember being immensely confused after reading some Transformers comics back in the day (early eighties) when I was going super hard on the animated series (G1). The comics presented a completely divergent timeline and I had no clue what to make of it.
Only later did I understand how that happened. And the same went for MASK, MotU and GI-Joe (basically all my childhood animated series

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But this phenomenon was never confined to comics; the same thing happened to novels as well.
First one coming to mind is Splinter of the Mind's Eye. At the time published as the official continuation of the Star Wars storyline after the release of the first film (later dubbed A New Hope), before The Empire Strikes Back was even an idea. It was later even retconned away completely.