There are multiple examples of additions by mystics to the siddur and machzor and to the practices concerning how and when the prayers are said. The following are a few examples.
Additions to the Shema
The several sections from the Torah which the siddur and machzor call the Shema are recited in the morning and evening service. Based on the view of the mystical book Zohar, mystics felt that the total number of words should total 248 the traditional number of positive commands in the Torah. Since the words in the several sections do not add up to 248, the mystics developed a system to reach this total, depending on whether an individual is reading the Shema, or it is part of a service conducted with a chazan, cantor, who generally keeps the synagogue attendees praying in unison by reciting where the ending of prayers loud.
If a person is reading the Shema without a chazan being present, the individual should add the words el melech n’eeman at the beginning of the Shema and add a fourth word emet at the end. The three words are not added when there is a chazan.
When there is a chazan who ends the prayers, the chazan reads the last words of the Shema without adding emet silently and then adds Adonai eloheikhem emet loud.
There are two problems with this practice beside the idea that Jews should add to the wording of biblical passages. First, while the individual adds four words, the chazan only adds three. The three added by the chazan and heard by the congregation substitutes for the omission of el melech n’eeman. But by only adding three words, the chazan does not reach the desired goal. Secondly, and more significantly, the total number of words in the Shema read by individuals, counting the additional four is 247, not 248.
The two loaves of bread at the Shabbat meal
A reasonable explanation why many Jews set the Shabbat table with a white table cloth, place two loves on the table, and cover the two loaves with a decorated white cover is that it reminds the family of the miracle of the manna that fed the Israelites during the forty years in the desert. No manna fell on the Shabbat. On Fridays, two portions fell, for Friday and Saturday, recalled with the two loves. The manna fell on white dew and was covered with white dew, recalled by the white table cloth and the covering of the loaves.
Many mystics insist that both loaves should be cut. Since they ate three meals on the Shabbat, Friday night, Shabbat noon, and the seudah shelishit, the additional third meal in honor of the Shabbat, and wanted to start the meal with whole loaves, they needed six loaves.
The kiddush over wine during the day of Shabbat
The ancient practice was to simply say the one sentence prayer before drinking the wine for the kiddush of Shabbat day. Isaac Luria instituted the practice to say additional words before the blessing. While the rabbis stated that one must drink a sizable amount of the wine, and while the general rule is that one must say a beracha achrona, a blessing after drinking wine, one does not do so after this kiddush. This is strange since it appears that the drinking of wine is not part of the meal and should not be included in the blessing after the entire meal. This seems so since after the drinking of the wine, the family washes for the start of the meal and the meal is introduced by the blessing over the loaves of bread. Why is there no beracha achrona?
It seems to me that despite appearances, the drinking of the wine is an integral part of the meal. We drink wine at the Shabbat meals to add to the joy of the Shabbat day and the meal.
 Scholars date the Zohar to around 1290 and state it was composed by Moses d’Leon, while many mystics claim it was composed by Simeon bar Yochai around 130 CE.
 In the third century CE, Rabbi Simlai invented the notion that there are 613 commandment, 365 negative commands and 248 positive ones. This is recorded in the Babylonian Talmud Makkot 23b. The Talmud states derash rabe Simlai, Rabbi Simlai delivered a sermon. He developed the sermon to emphasize that a Jew should observe the biblical commands with all the bones in the body (248) every day of the year (365). The sages recognized that this number is incorrect, but the idea caught on with the people, and even Maimonides helped the people by listing and explaining all the 613 commands that the consensus of rabbis felt were explicit or implicit in the Torah.
 Siddur Eizur Eliyahu K’minhag Rabbenu Hagra, Michon Keren Eliyahu, page 38-40.
 The word emet is the first word in the following prayer.
 Babylonian Talmud 106a.
 Siddur Eizur Eliyahu K’minhag Rabbenu Hagra, Michon Keren Eliyahu, page 251.