They also mentioned that the pym particles are driving the bad guy nuts and all his evil actions are the result of some kind of psychosis.
It feels a bit like a subplot was cut with the particles influence on one's mental health.
Possibly because they decided they did not want to make it an issue for Scott, but couldn't cut the line with the suit taking it's toll on Pym and Cross.
They might have meant to use that later to explain Pym's volatile behavior he is known for in the comics.
Dr Pym mentioned that the Ant-Man helmet shielded the user from the effects. Maybe not totally or Dr Pym made that breakthrough after using the technology in combat himself.
It's possible he was talking about the mental problems casued by using the suit, but I think it's more a matter of the stress that was put on his body over the years. There was a time in the comics when he was confined to 10 feet and called himself Goliath, the stress from going to being Giant Man to Ant-Man was the cause.