Cannot connect to some devices while connecting via Wireguard

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Hello I have a following network devices:

  • R1: router Mikrotik hAP AC3
  • S1: managable switch Dlink Smart DGS-1100-05PDV2
  • R2: router (which acts as switch) Netgear WNR3500L v2 with FreshTomato firmware
  • AP1: access point TP Link EAP225

My network is divided into two sub-networks:

  • N1: 192.168.3.0/24
  • N2: 192.168.5.0/24

and two vlans:

  • vlan-main (VID 101) -> N1
  • vlan-iot (VID 102) -> N2

Device wiring's presented on the imagetopology On the main router - R1 I have configured Wireguard in order to be able to connect to my network from 'outside'. It works fine except one thing, which is the reason why I created this question.

When I'm connected directly to my LAN network either by wifi or cable I can access all the network devices without any problem. By accessing them I mean that I can open their web interfaces.

But... When I'm connected to my network through Wireguard I have access only to R1 and S1. I'm trunking all the traffic from R1 to AP1, because this AP is able to handle vlans - it broadcasts two wifi, "main-wifi" which is "connected" to vlan-main and "iot-wifi" which is connected vlan-iot.

Configuration on the AP is quite poor... the only thing that I can set on this device regarding management is "management vlan" which in this case is vlan-main.

What is the problem here? Did I forget to set something on Mikrotik? Did I miss some settings in the Wireguard's configuration?

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