Internal party power struggles, gerrymandering, demanding photo ID from people in poor areas who rarely have that sort of identification, etc, are all various ways to try to influence the outcome, and some of them are pretty disgraceful. I think it's fair to discuss and criticise the way elections in the US are set up.
Let's not kid ourselves here though: when Trump says that the election is rigged he's specifically referring to voter fraud and has identified the two main culprits on several occasions. One of them is the government, who supposedly take your republican vote and turn it into a democratic vote instead. The other group is blacks and various other minorities who will vote "13 or 14 times" because they're all dishonest criminals who live in one big favela where there's zero regulation or transparency when it comes to voting. It's a very dangerous, fascist idea to peddle around, with little other purpose other than to undermine democracy itself.
In fairness to Trump, republicans have been actively trying to spread the myth of the rigged election since long before he emerged.