@Jakub007,

Can you provide a bit more info about what hardware you are using and how your network is laid out?

MAC addresses are unique identifiers for a device and they should always be the same across networks - unless it is being randomized due to privacy reasons.

From the sounds of it, you have two separate "Routers" on your network, which are conflicting with each other when looking at your network from higher up in the chain. You may consider a IP-MAC binding so that the IP address and MAC addresses will align between your two networks, however, this will likely be the case unless one of the two networks can be configured as an Access Point, or your switches can combine the two networks into one. If you provide more info, I may be able to provide some additional insight.