I find it hard to imagine that there are connectors in which the Male pins are not supposed to match with the corresponding Female pin numbers.
What software and connector type do you have in mind?
There can be a difference between the representation of how a symbol for a connector looks on a schematic and the location of the pins on the Footprint of the PCB.
Are you sure you are not mistakingly looking at mirrored representation of the connectors?
I once had to cut the wires of an 14 pin IDC cable with a knife and swap the even and odd wires because they layout of an LCD connector was designed to be inserted in the front of the LCD, but there is of course a frontpanel in front of the LCD, so the IDC connector was soldered into the back of the LCD.
Shit like that happens all the time. It seems to be an intrinsic part of life as we now it.
There are some rare hermafrotitic connectors, where any can be mated with any. Those were used in old IBM computers (Was it the 360?) and I think also with GPIB, but I'm not sure.
Lately USB-C is gaining popularity. Not hermafroditic, but plugs can be rotated 180 degrees.
The power pins are symmetrical over the design, also because multiple power pins are good for reliability and current handling capability. Current computers have enough smarts to figure out how the signal wires are connected.
But for ordinary connectors, if M & F pin numbers don't match then probably (& in this order):
1). You made a mistake.
2). There is a mistake in your libary symbols.
3). Something weird and/or unsual is going on, and it is intentional (for a good reason?).