This not a duplicate of MCPE-131325, which is about desync weather between server and client. But this issue is a bug of /weather command.

Run "/weather rain 60" and wait three seconds, the weather does become clear both on server and cilent (can confirm with fire or cauldron), but the command says it's thunder.

I guess this is caused by that thunder timer is reset to a  non-0 number after three seconds. So both clear timer and thunder timer works, and the command says it's thunder.

Step to reproduce:

1. Run "/weather rain 60"
2. Rains. After 3 seconds, the weather becomes clear.
3. Run "/weather query"
4. It displays "thunder"

Expected behavior:

It displays "clear" when the weather is clear.