If I read the Google translation of the Russian correct your problem you are having is with stray fragments of video being left behind when editting.
This is a common problem and is often caused by adding an object in the plan, which separates a small portion of the object that is close by.
To find these fragments, you must zoom in on the timeline where you happen to see them, and then delete them.
I do not have any .TS files myself so I downloaded a 321 MB sample ed24p_10.ts from http://www.w6rz.net/ (as a ZIP).
In MEP 2013 I set a new project to 1920 x 1080,24 fps and imported the TS file.
I split it roughly into thirds with two cuts and then deleted the middle part as you described.
I exported it as 920 x 1080, 24 fps. I imported that into MEP 2103 and examined the join. It was as it should be, with a distinct switch from the end of Part 1 to the start of Part 3. There was no frame from Part 2.
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Are you sure you have the fps settings correctly matched in all cases?
If you still get the problem you should upload a small TS file that exhibits it so that we can again try to reproduce.
However, if you only get this issue with very large files (3-4 GB) then that is too big for me to work with and you should seek help from Magix. To avoid a language problem, refer them to this post.