The simple answer is yes, at least apparently so, although sources are somewhat scant.
Check out this archaeological discovery from Israel (see also here for more cool photos).
I find the incense shovel especially interesting since most people seem to be unaware of the post-temple use of incense in Jewish Synagogues across the Mediterranean.
Below is a copy of an exhibit of artifact from Jewish Egypt.
In the Middle Ages we have the famous exhortation from the medieval Karaite sage Sahl ben Mazliah Hakohen against the Rabbanites who pray and light incense at the grave of Rabbi Yose Haglili
ואיך אחריש ודרכי עובדי עבודה זרה בין מקצת ישראל, יושבים קברים ולנים בנצורים, ודורשים אל המתים, ואומרים: "יא ר' יוסי בגלילי (בדלתון) רפאני, הבטינני (תן לי הריון)", ומדליקים הנרות על קברי הצדיקים ומקטרים לפניהם על הלבנים וקושרים עקרים (או עקדים) על התמר של הצדיק לכל מיני חלאים וחוגגים על קברי הצדיקים המתים ונודרים להם נדרים וקוראים אליהם ומבקשים מהם לתת להם חפצם."
How can I keep silent when Jews follow the custom of idolaters? They sit among graves of saintly persons and spend nights among tombstones, while they seek favors from dead men, saying, “Oh Jose the Galilean, grant me a cure!” or “Vouchsafe me a child!” They light lamps at the graves of saints and burn incense upon the brick altars before them and tie bowknots to the palmtree bearing the name of the saint as a charm for all kinds of diseases. They perform pilgrimage rites over the grave of these dead saints and make vows to them and appeal and pray to them to grant their requests. (Quoted in Nemoy, Leon, Karaite Anthology pp. 115-16)
As you can see, from this book by Richard Freund, during the time of the Karaite Hakham Daniel Al-Qumisi, there was a Rabbanite-Karaite polemic regarding the use of incense in the Synagogue (although the whole thing seems unclear and somewhat bizarre; I am not averse to the possibility of Freund having committed an error here)
I find it very hard to believe that this conflict has anything to do with the Temple incense (i.e. that the Rabbis were contravening an explicit written [and oral!) injunction that prohibits using the temple formula outside of the temple). So what was this all about?
Also interesting is the mention in the Talmud of the burning of ketoret as part of the mourning ritual for Rabbi Yehuda Hanassi.