I have two CRS226 switches set to bridge mode.

Switch1 has ip address 192.168.88.3
Switch2 has ip address 192.168.88.4

When I cable them together using one SFP port, I can access both webUIs if I have the laptop plugged into either switch.

If I cable the second SFP ports, I can't access either webUI, regardless of what switch I am attached to.

If I remove the SFP ports from ethernet1-master and bond the SFPs together, I can access the webUI if I am attached to that switch, but I can't access the webUI on the other switch.

I am new to Mikrotik and I can't figure out why (or even how to test) what the issue is.

Since you're using bridges, you need to enable Spanning Tree Protocol. By running redundant links between the switches, you're creating a switching loop. Turn on STP, and it should clear up. Or, disconnect one of the links, set up your bonding interface to include the two SFP's, and then reconnect the second link.