When we say G-M406 (G2a2b1), we are referring to a mutation (SNP) that was carried by a man who lived 10,200 years ago, likely in Anatolia or Northern Syria. All male lines bearing the G-M3302 mutation, descended from this man, however, not all G-M406s are G-M3302. You can view the current G-M406 YFull tree here. Click here for FTDNA's Discover Tree for G-M406.
When an ancient sample is listed as G-M406 or FGC5089 for that matter, it does not necessarily indicate that the sample is ONLY G-M406. But rather that the coverage (or amount of YDNA able to be extracted) doesn't allow us to determine a more specific lineage. Essentially, the analysis produced SNPs that were sufficient to confirm G-M406 (or G-FGC5089) but nothing further is known. Therefore these ancient samples COULD fit into any one of the known G-M406 subclades, or could possibly belong to a previously unknown subclade. Unfortunately, we may never know. Still, most G-M406 and essentially all G-FGC5089 seem to have occupied the same territories from the Neolithic into the Middle Bronze Age and possibly longer. And even though these samples are not refined, they can still inform what we know about G-M3302.
G-M406 men gained enough traction around 9,000 years ago that additional lines began to branch off starting with two main groups G-FGC5089 and PF3293/PF3316. These men still are considered G-M406, but because they developed additional SNPS, we are able to refine their lineage further in history. About 6,000 BC, G-FGC5089 eventually produced men bearing G-FGC5081 and G-M3302 SNPs, further branching the G-M406 lineage. The same can be said for PF3316, who produced G-Z6029 and G-Z60348 around 5,200 BC.