Of course Vanguard plays games. They all do, the question is which games and how well they play them. For example, Vanguard lends securities. A few, not all. And I believe that Vanguard plows all the earnings from that practice back into the funds, as opposed to some other managers who take a cut.
https://advisors.vanguard.com/iwe/pdf/Sec_lending.pdf (Vanguard practices)
https://personal.vanguard.com/pdf/icrsl.pdf (variations with risks and benefits)
Then there's sampling. Usually full replication is used for S&P 500, but sampling is often used for funds that include smaller cap stocks. Both POMIX and VTSMX use sampling. Different managers, different samples.
Then there's the question of which index they track. Even if over time two indexes for the same market segment do about the same, there can be a fair amount of difference from year to year. POMIX and VTSMX track different indexes.
Then there's the question of timing. Some families have rigid rules about when they must add/drop securities from their portfolios. Others are a bit more flexible, which allows for slightly better (or worse, if poorly executed) performance, but at the expense of slightly greater tracking errors. (This is a feature I checked
years ago; I don't know if some funds still allow greater leeway.)
Then there are quirky attributes. Most funds immediately put the cash they receive from portfolio dividends to work. But SPY is prohibited from doing this because it is a unit investment trust. The fund must hold the cash; it's only when the cash dividends are distributed and you buy more shares through your broker's reinvestment program that this money gets put to work (quarterly).
I vaguely recall an S&P 500 fund many
years ago (Safeco? Transamerica? X??) that said it tracked 499 stocks, excluding its own. Index funds are not necessarily the simple vehicles people expect.
Lots of reasons why the performance of index funds diverge - from each other and from their theoretical returns (index return less expenses).