I didn't have this issue when I was using ver 1.580.3.
After upgrading Jenkins ver 1.609.1 (together with other Jenkins plugins update),
I started to see this issue.

My jenkins job is using multi-config project type (aka Matrix project),
and has 3 variants.
I didn't set to be run concurrently,
so the 3 variants will start the build one by one.

In the previous version 1.580.3,
it will reuse the same workspace folder for all of 3 variant builds.

In the new version 1.609.1,
when multiple jobs are triggerd,
I can see sometimes the first variant build of the second job
will start to create and use workspace@2
instead of re-using original worksapce.

Note:
I'm also using disk-usage plugin.
At the end of build,
it will trigger that plugin to calculate workspace disk space.
My work space tends to be large and sometimes it take several minutes to finish.

I suspect it's that disk-usage plugin still occupying the original worksapce,
but the second job in queue starts earlier,
so it creates workspace@2 for the first variable build.

From workspace@2,
I always see only one variant only under AXIS folder.