I don’t blame Filoni for the discrepancies between The Clone Wars and the Clone Wars Multimedia Project. However, I do think spending too much time around George Lucas may have negatively influenced him.
At first, Filoni wanted to tell a completely different story, centered on an original cast of characters who’d go on adventures at the edges of the galaxy, far from major figures like Anakin and Obi-Wan. He didn’t want to heavily involve the main characters because, in the beginning, he cared about continuity and wanted to avoid contradicting the Republic comics and other materials from the Multimedia Project. But George Lucas wasn’t fond of that idea and pushed for the series to focus on the film’s main characters, which inevitably led to contradictions with previously published material. So I don’t blame Filoni for these inconsistencies, because he genuinely tried at first to create something new while respecting the existing canon.
That said, I’m convinced that over time, being so close to George Lucas changed the way he looked at the franchise. While he initially seemed interested in preserving continuity and avoiding major contradictions, spending so much time with someone who famously said “continuity is for wimps” must’ve shifted his perspective. It turned him into someone who, much like his mentor, doesn’t care much about consistency within the universe, which explains his disregard for previously established continuity (whether it’s Legends or Canon) in later years.