Hello,
The pin_mux component provide configuration of pins for all devices of the target MCU. When you select just a direction of pin without any routing to a device it is not possible to set the direction. In addition, when you route a pin to a device, the device can provide setting of the direction (e.g. TxD pin of the UART is output).
The first warning is not a bug.
Please note, that the Collapsed View Mode (in the Component Inspector of the PinSetting component) displays routing of pins for every device separately. It also means that you can select one pin for two devices - this is a conflict because one pin can be routed to one device only. This case is reported as a error in the settings.
You can configure the routing by using the PinSettings component (pin_mux) or by another component (e.g. Init_FTM). When you select a pin of FTM CH0 in a Init_FTM the routing is visible in the PinSettings component too. This pin cannot be routed by any other device (e.g. GPIO).
See for example the following case that demonstrate the conflict of the settings (the error is reported correctly):

If you have a different problem, send me the details of the issue (how to reproduce the problem and the project if possible), please.
Best Regards,
Marek Neuzil