At the very end, when the 5 o'clock whistle blows, both time cards are in the appropriate 'In' slots. When the scene eventually cuts to Ralph and Sam clocking out, Sam is in the process of clocking out, and Ralph's card is in the 'Out' slot. Sam clocks out and puts his card into the 'In' slot. Then Ralph takes his card out of the 'Out' slot, clocks out, and is in the process of inserting his card into the 'In' slot as the scene fades to the long shot of the two heading home. The cards should have been in the 'In' slots as they were when the whistle blew, and the cards should have ended up in the 'Out' slots after the two clocked out.
When Ralph uses the mini-rocket with a loop of rope to carry Sam away, there is no way that the rope could have gotten around Sam and under his front legs/arms. The way Sam was sitting, the rope would have merely slipped over and by Sam, not snaring him.
There is a shot of Sam's and Ralph's time cards. On Monday, Sam punched out for lunch at 12:00, but punched back in at "11" -- apparently an hour earlier than when he punched out, although the punch-in time after lunch lacks the digits for the minutes. The error -- less obvious -- is repeated on Tuesday: Out at 12:02, in at 12__.