The First Time / The Wedding Part II
In Season Two's season finale, "The Wedding Part II" it is Debra who introduces Father Hubley to Ray. However in the season six finale "The First Time" it appears Father Hubley is the family priest of the Barone family (and has been for a long time), and this time, it is Debra who is introduced to Father Hubley by Marie.

The Gift / Debra Makes Something Good
In the Season 2 episode, "The Gift", Frank celebrates his 65th birthday but in the Season 4 episode "Debra Makes Something Good" he says he is 64 years old.

Ray Home Alone / The Kicker / A Vote for Debra
Robert's supposed bedwetting problem was exposed as a prank perpetrated on Robert by Ray in "Ray Home Alone". Nonetheless, in "The Kicker" Robert still says that he had a bedwetting problem. Again in "A Vote for Debra" Marie says that she would never deny her kids water and Frank replies by saying that that would explain Robert's bedwetting problem.

Meant to Be / High School
Robert makes out that he was unpopular growing up in "Meant to Be" however in "High School" seems to be a very popular person.

The Wedding Pt1 / 10th Anniversary
In "10th Anniversary" it is snowing outside, but in "The Wedding Pt1” the date that they book for the reception is on the 17th of June.

The Wedding / Diamonds
In "The Wedding" Debra is ecstatic at the engagement ring Ray gives her, and says she can't wait to show her mom. However in "Diamonds" she confesses she had the diamond in the ring changed (to her grandmother's stone) so that her parents wouldn't think less of Ray.

The Nice Talk / The Wedding
In this episode, Ray tells Amy's mother that Debra no longer reads his column, although she did when they were dating "and she was wooing me." But in "The Wedding", Ray proposed to Debra in his very first column - so when they were dating, he didn't have a column.

The Pilot / Mia Famiglia / Recovering Pessimist
In both "The Pilot" and “Mia Famiglia” it is seen that Ray receives a lot of awards for his writing, but in "Recovering Pessimist" Ray says he has never won an award.

Recovering Pessimist
In "Recovering Pessimist", Ray is nominated for a Sportswriter of the Year award, but he didn't think he will win. He rattles out of the names of the writers he is up against, and among those he named was "Chuck Heaton", from Cleveland. Debra, in an attempt to build his confidence, tells him he's better than the other nominees, and singles out "Chuck Heaton" as being terrible. It just so happens that not only is "Chuck Heaton" a sportswriter (now retired) from Cleveland, he's also Patricia Heaton's father.
Halloween Candy
In "Halloween Candy", Frank dresses up as Frankenstein. This is an in-joke to the role he played in the movie Young Frankenstein (1974)

The Sister
In the episode where Debra's sister comes to visit, The Sister, and announces she is a nun Debra gets upset at all the family members making a big deal about it. Marie comes over with a cake shaped like a cross. In almost all the scenes where the family is sitting at the table different pieces of cake are missing. In some of the camera angles there are no pieces of cake cut from the bottom yet when the cake is seen from other angles there are.
In" T-Ball", Ray puts the snacks in a blue bag. But when they get to the field, the snacks are in a different bag.
In "Baggage" the big fork and big spoon are different to the set shown in earlier seasons, and have switched positions.
In "Ride-Along", Robert chides Ray into accepting his offer to go on a citizen's ride-along. They are initially sitting on the couch at the time, and when they rise, if you look closely behind where Ray is standing, through one of the kitchen windows you can spot a production crew member.