Hi Phil, looks like a bug in shell, unfortuantely shell is one of the less robust areas of the geometry library that MoI uses so it's not particularly unusual for it to need some manual cleanup work for its results. Shell for thickening an open surface also usually works best for thickening an entirely smooth piece, it can have a lot of problems with dealing with an open surface that has sharp corners on it. Usually for something with sharp corners it's better to have a solid and then use Shell to hollow out the solid rather than trying to thicken an open surface. That's because with the solid case it tends to be easier for side walls to be constructed from existing objects rather than needing them to be cooked up completely from scratch. See here for some discussion on this:
http://moi3d.com/forum/index.php?webtag=MOI&msg=5633.3

In your particular case here my best guess is in that problem area you've circled that the offsetter has decided to extend and reintersect those edges and done a kind of bad job of that process so that the offset edges don't match up very well to the original ones.

You'll need to repair that area by deleting the weird looking surfaces there, and then constructing a new piece to fill in that area which can be done in this case by selecting the 2 edges above, running Construct > Extrude to extrude a shape downwards, snapping on to an endpoint of one of the bottom edges to get the proper extrusion height, and then joining those pieces together.

There's also some badly formed areas on the hole area on the left hand side, those will also need a couple of pieces to be deleted, rebuilt, and joined in order to make a proper final result.

- Michael