I see the same thing. I don't know if this is inherent in how the underlying Linux facilities handle packets.
I, too, was surprised that queue changes drop traffic for a second, and so were my customers. I can change queue parameters on Cisco and Juniper on the fly and outside of the expected drops when I lower queue capacity traffic is not affected. Increasing queue size leads to no packet drop whatsoever.
Sometimes I have to increase queue sizes on the fly, particularly when a customer asks for an increase in bandwidth and wants it done immediately. I sell short lived connections, and by tomorrow the customer may no longer be on the premises.
That said, I can work around it by just warning customers and getting write off so it is not a big deal.
Specific answers require specific questions. When in doubt, post the output of "/ip address print detail", "/ip route print detail", "/interface print detail", "/ip firewall export", and an accurate network diagram.