The matter is complex; here is a brief explanation.
The extant manuscripts of Scripture, being ancient and often fragmentary, are not always in agreement. And, as might be expected, textual critics do not always concur as to which manuscript or fragment best represents the original (which is termed the "autograph"). Nor is this a modern-day phenomenon. From the earliest days of the present Church Age, manuscripts have been copied by men whose care and skill in transcription is less than perfect; and, regrettably, some of their imperfect copies today are among the most ancient extant manuscripts.
Complicating matters is that some of copies originated from men who lacked respect for the Scripture, and felt free to make alterations. One of the best-known examples of this is the account of the woman taken in adultery, John 8:3-11. There is general agreement among scholars that the passage is spurious.
Another egregious example is verses 14 through 26 of Chapter Thirteen of the Prophecy of Jeremiah. Those verses are spurious, being found only in the Masoretic Hebrew Text. The fact that they are spurious should be apparent to almost any reader, for they falsely assert that the Levitical Priesthood shall function in perpetuity. That claim is easy to disprove; consider, for example, the Seventh Chapter of the Epistle to the Hebrews, which explains that, upon dissolution of the Old Covenant and inception of the New Covenant, the Levitical Priesthood was supplanted by the priesthood of Christ Jesus, who is a priest after the order of Melchizedek.
A translator typically works from a particular critical edition of a each book of the Bible. And a publisher may specify for each book that a particular critical edition be followed. Thus, the reading of the Bible published by Acme Press may differ from the reading of the Bible published by Zenith Press.
Sadly, the pre-Incarnation Scripture (commonly mis-termed the "Old Testament") of most English Bibles is translated from the Masoretic Hebrew Text, rather than from the Septuagint. And though use of the Masoretic Hebrew Text does circumvent the problem which you cite, it introduces other problems of a more serious nature.
Keep in mind that pre-Incarnation Scripture has been preserved for a purpose, Romans 15:4, I Corinthians 10:11. And though from our limited perspective, it may appear that the preservation is imperfect, we may be confident that the Lord God has preserved all that is necessary to provide for us the needed instruction, example, and exhortation.
Concerning Scripture written by the Apostles following the Incarnation, there is virtually no question as to the reading of the autographs.
Back to the Prophecy of Jeremiah: For any given passage, the Septuagint reading is more reliable that is the Masoretic Hebrew Text reading, for the Masoretic Hebrew Text is a counterfeit of the Ancient Hebrew Text, of which no copy is extant.