The main problems it caused were that it was introduced into popular packs in a time where there wasn't a wide knowledge base on crafting packs yourself or many options for modpack selection. Launchers weren't user friendly for customization. Plus the popularity of packs was driven largely by YouTubers who jumped on the FTB train.

It caused problems because you'd play mods one way and then try a pack with GT and run into weirdo recipe changes and blocks to mods.

What didn't help anything was the completely toxic nature of the IC2 forums back then, which was the main repository for Industrialcraft knowledge. This played a huge part since IC2 was the only ticket to jetpacks and the main mod for ore processing. Thermal grew and supplanted, but back then you were stuck with jerks who'd dogpile on a simple question. It was an era of elitist trolls that pissed people off for fun.