Third Call to Prayer (Adhan)
When the Messenger of Allah used to go to the mosque for the Friday prayers, the person in charge of giving the call to prayer would first call the adhan and then the iqamah, and this practice continued during the caliphates of Abu Bakr and Umar and for half of the caliphate of Uthman. However, in the seventh year of his caliphate, Uthman ordered that a third call to prayer be given. This shocked the Muslims because they considered the addition of a third adhan to be a bidah (religious innovation).
Al-Yaqubi comments in his history that Uthman had the audacity to climb the pulpit of the Prophet and sit in the same place that the Prophet used to sit in, even though Abu Bakr and Umar respected it by never sitting on the pulpit of the Prophet. 
Complete Prayers in Mina
During the Hajj (the Pilgrimage), the prayers in Mina used to be performed in the shortened version (qasr) by a person who was traveling. However, one year, Uthman recited the prayers in their full form rather than in their shortened form. Many of the companions protested and one of them, Abd al-Rahman b. Auf came to Uthman and asked, “Didn’t you pray with the Prophet in this spot with two rakats (units of prayer)?” Uthman said he had. Abd al-Rahman b. Auf then asked, “Didn’t you pray with Abu Bakr in this spot with two rakats?” Uthman said he had. Abd al-Rahman b. Auf further asked, “Didn’t you pray with Umar in this spot with two rakats?” Uthman said that he had. Abd al-Rahman b. Auf continued, “Didn’t you, yourself lead the prayers during your caliphate in this spot with two rakats?” Uthman said that he had. Abd al-Rahman then resorted to ask why Uthman had read the prayers with four rakats this time, to which Uthman replied, “I have married a woman from Mecca, and the people of Yemen came to me and said, Uthman is a resident of Mecca, but he still prays qasr even though he should pray the complete prayers; because of this, I wanted to do four rakats.” Abd al-Rahman b. Auf then pointed out to him that the Holy Prophet himself was a resident of Mecca and he still led the prayers with two rakats, and that Uthman should follow the tradition of the Prophet. Uthman replied, “This is the opinion that I have followed.”
In another case, when Uthman was in Mina, he became ill and asked Ali b. Abi Talib to lead the prayers. Ali replied, “If you like, I will lead the prayers, but I will pray exactly the way that Prophet Muhammad did (the shortened prayers).” Uthman objected and told him that he had to pray with four rakats, and the matter was left at that.
Khutbah before the Eid Prayer
Throughout the time of the Prophet and the caliphates of Abu Bakr and Umar, as well as today, the khutbah (sermon) on the day of Eid is said after the Eid Prayer. However, Uthman noticed that people tended to miss the prayers, so he developed the habit of giving the sermon first, and then after that leading the prayer.
Land of Fadak and Marwan b. al-Hakam
Aside from encouraging Marwan b. al-Hakam to return from exile and making him his son-in-law, Uthman also granted him the land of Fadak.
Originally, the Prophet gave Fadak to his daughter Fatima al-Zahra because when the ayah of the Qur’an was revealed, “And give to your kin their right,” (c. 17:26) the Angel Gabriel told the Prophet that he had to give Fadak to Fatima. However when Abu Bakr assumed the caliphate, he held that it was fay (income for all of the Muslim community), so he took Fadak away from her and made it a public endowment, while the Ahlul Bayt maintained that it was a private gift. Irrespective of which viewpoint one takes, Uthman still had no right to grant the land to a specific individual, since neither public endowments, nor private property of someone else can be given to a private party.
In addition to Fadak, as mentioned earlier, Uthman also gave Marwan all of the income from Africa. Such treatment raised discontent among the Muslims of Madinah because Marwan was not an admired or moral figure.
 Ansab al-Ashraf, 5:39; al-Muntazam, 5:7
 Ibn Abi Shaybah, al-Musanaf, 2:48; Al-Zuhai; and others
 Al-Yaqubi, 2:162
 Tarikh al-Tabari 4:268; Ansab al-Ashraf, 5:39
 Ibn Hajar, Fath al-Bari, 2:261