I am mainly trading SPX/NDX and MES/MNQ - I have seen some brokers adding mark up on exchange fees (instead just passing those fees to clients) Is this legally allowed particularly when they claim these are just passthrough fees.
Brokers can charge any fees they want to as long as they disclose the fees. Just outright state which brokers and what the fees are. I know of only one broker that does not pass on the CBOE SPX option fee.
It's legal as long as they disclose it. And, It's probably even worse than you think since the fees you are seeing are not what the brokers are really paying - they get discounts and rebates.