This seems to happen because of the new XKB symbols file bn which was created as a fix of this bug. As far as I can tell that file is redundant, since the name of the layout - Malay (Jawi) - is already present in the symbols file my. Currently there are two entries named Malay (Jawi) in the list of input sources.
Anyway, removing or renaming the bn symbols file seems to fix this issue.
cd /usr/share/X11/xkb/symbols
sudo mv bn bn.bak
Edit:
I filed this bug, which has been accepted and will affect version 2.21 of xkb-data.
Edit II:
The issue is also about to be fixed in v2 of ibus-avro.
Edit III:
It seems moving the file make wayland session on latest Ubuntu inaccessible. Also the developers of ibus-avro suggested another workaround which fixes the issue without interfering with wayland session. This is documented here
In short, you need to edit the file at /usr/share/ibus/component/ibus-avro.xml
sudo vim /usr/share/ibus/component/ibus-avro.xml
On line 20, change
<layout>bn</layout>
to
<layout>us</layout>
Save the file and restart your session.