Trump is suggesting that actual votes are being miscounted deliberately. That the entire voting system of the US cannot be trusted to provide the result the public give it. That's a very different charge, a very dangerous one, and utterly unproven.
His railing against the system regards economics and yes the foray of money into politics. It is in a similar category of statements but is very different than claiming the voting machines are rigged. Yes, some Bernie supporters alleged there was outright voting manipulation, but the Sanders campaign did not directly allege that.
But between the Dems and the Reps? Those two are fairly balanced. There is some rigging in some states through gerrymandering and making it harder for some groups to vote, but it's on a very different scale than the rigging towards the two-party establishment.
> We now have a political situation where billionaires are literally able to buy elections and candidates. Let’s not kid ourselves. That is the reality right now. [1]
(He also is fond of claiming "the system" is rigged, if not elections directly.)
[1] https://www.washingtonpost.com/politics/sanders-takes-on-bil...