Hebrews 9:4 contains an apparent error regarding the placement of the golden altar of incense IN the Holy of Holies. William Lane’s World Biblical Commentary. Lane seems to argue that the error crops up due to the author of Hebrews using the Samaritan Pentateuch. Quotes:
The location of the xpuoouv… Ouμlatń plov, “golden altar of incense,” within the Most Holy Place is problematical because it was well known that it stood in the Holy Place just before the inner curtain (Exod 30:6; 40:26; for the history of this altar see de Langhe, Bib 40 [1959] 476-94). The scribal tradition represented by Codex B and certain of its allies recognized this problem and sought to resolve it by textual alteration.

The ceremonial prescriptions for the Day of Atonement, however, plainly indicate that this altar was located in the Holy Place (Lev 16:18; for the ministry at this altar see m Tamid 1:4; 3:1, 6, 9; 6:1), and this is confirmed by sources contemporary with Hebrews (Philo, Moses 2.94-95, 101-4; Who is the Heir? 226; Jos., J.W. 5.216-18; Ant. 3.139-47, 198; Luke 1:8-11).

The description in v 4 corresponds to the Samaritan Pentateuch recension of Exodus, in which Exod 30:1-10 is inserted between Exod 26:35 and 36. This was one of the factors that led Scobie to deduce that the writer of Hebrews was representative of Samaritan Christianity (‘The Origin and Development of Samaritan Christianity,” NTS 19 [1972-73] 412-13).

The correspondence should be seen rather as evidence of the variety of text-types extant before the standardization of the MT. Although no Greek text reflecting the proto-Samaritan text of Exod 26 has as yet been recovered, it is probable that the writer of Hebrews was following this textual tradition.
The only other way to assuage the harshness of the supersessionism would be along the lines of the following, offered by Pamela Eisenbaum, in the Jewish Anotated New Testament: In recent years, some scholars have made efforts to address the problem of anti-Judaism in Hebrews and have attempted to offer an alternative lens for reading Hebrews’s disparaging comments by means of attending to their historical context. For example, if Hebrews is written after the destruction of the Temple, the language of supersessionism can be viewed not as a prescribed attack on Jewish ritual practice but rather as at attempt to cope with the desperate reality that, in fact, worshipping God by means of the Temple cult is no longer an option. Framing Hebrews this way analogizes it to the Mishnah, where the absence of a Temple necessitates translating the complex of Temple cult practices into other forms. There remains, however, a difference. The Mishnah never disparages either Israel’s past ritual practice or the institutions that sustained those practices, like the Temple and the priesthood. Part of the agenda of the Mishnah may have been to provide guidance about the observance of Torah in the absence of a Temple, but it does not do so by lamenting that the past practice was inadequate or misguided the way Hebrews does.