Is there a way to fox small adjacencies without using auto-align. When I use auto-align the other geometries of the shape gets affected in a way not intended to.
Yes. You can use the other commands such as align and pull to room to fix the issues with a higher level of control, you can also use the Use Anchor Lines and Constrain Group Boundary options of the Auto Align command to control the unwanted changes. Here is a short recording that reviews these options.