Knifeツールについては度々修正がされています。
2.69RC1直前の10/4〜11/9までに11件の修正が加えられています。

使用されているリビジョンが書かれていないので列挙しておきます。
このツールに関しては今使用しているバージョンでの挙動を正とするのがいいかと思います。
明らかにバグと言えるものは別ですが・・・。

r61204: knife tool: Remove unused 'extend' variable
r61203: knife tool: Clean up line hits when starting a new cut
　　　　 Fixes intersection points of the previous cut still being drawn when
　　　　 starting a new cut.
r61166: Fix knife bug exposed by valgrind.
　　　　 Was reading cage coordinate from those of existing
　　　　 BMVerts even for newly created verts that don't
　　　　 have cage coordinates there.
r61144: Rewrote a lot of knife tool. Now allows cut-through
　　　　 to make new vertices in the middle of faces.
　　　　 This also fixes knife bugs:
　　　　 #36678, #35945, #35943, #35387, #35045, #35002.
r61045: Add 'cut-through' option for Knife Project operator.
　　　　 If enabled, it makes knife project act as the
　　　　 cut-through (Shift-K) version of knife.
　　　　 This option will soon be more useful when a better
　　　　 cut-though Knife change is submitted, allowing
　　　　 this to work for cuts within faces in addition
　　　　 to cuts across them.
r61016: remove return argument from wmOperatorType->cancel, was only ever returning OPERATOR_CANCELLED.
r60988: Fix #37152: Knife tool doesn't work properly with Maya preset (Zooming and Panning)
r60954: rename BM_vert_at_index -> BM_vert_at_index_find (since this searches the mempool).
　　　　 needed for other changes - coming.
r60720: code cleanup: utility function for getting a bool as a string.
r60670: add MEM_SIZE_OPTIMAL to avoid memory fragmentation & waste lost to slop-space.
r60544: fix for lasso selection (in non-zbuf mode) when the line intersected its self.
　　　　 isect_point_poly_v2() - add argument to check overlapping areas.