This is the way Sigil works in 0.3.4. It is by design. When you save an epub in Sigil 0.3.4 (or below), the opf and ncx is recreated. These files contain, besides other things, the TOC and the metadata. This was the only way the validity of the file could be garantueed. You could use the TOC editor in those versions to see what would be in the TOC. The original would be gone.
In Sigil 0.4 this is changed. By default the opf and ncx files are kept and not overwritten. That is great if you just want to edit an epub and want to keep the structure intact (including TOC). However, if you do more than that and the TOC will change, you have two choices. Edit the ncx of opf yourself to make it correspond to the rest of the epub or recreate TOC. That will change/recreate the ncx and opf again.
So basically, you have the choice. It is not a bug, it is by deliberate design.