A classic one was the new Thomas Cook branding, large graphic across the fuselage, where the placement of cabin windows on narrow bodies breaking up the characters made it look more that it was saying Thomson, their principal competitor.
Carriers in the 1950s found that having the upper fuselage of an aircraft white gave significant benefit to air conditioning loads, which was later forgotten by some (not all) design houses.
BMI got a substantial reprimand in an AAIB report into a near-miss at Heathrow with a lined-up aircraft, where the new matt blue/grey upper fuselage made it much less visible to an approaching lander.