Hot extrusion is the most common forming technology for aluminium alloy AA6061 due to its good extrudability, and thus it is important to study its high-temperature deformation characteristics. In this study, three abnormal features are observed in thermal-mechanical testing under extrusion conditions of AA6061 specimens from one billet: 1) Two types of specimens with grey-coloured surface or silver-coloured surface appear after solution heat treatment (SHT); 2) The silver-coloured specimens show orange peel surface after hot compression tests; 3) The silver-coloured specimens have lower flow stresses than the grey-coloured specimens. This paper investigates the mechanisms behind the above abnormal features. A laser scanning confocal microscope is employed to examine the surface roughening, and electron back scatter diffraction is used to characterise microstructural changes. It is found that the main causes of the above behaviour are due to different initial grain morphologies and the evolution of dislocation density after SHT. The silver-coloured specimens initially have smaller columnar grains which undergo recrystallisation and extensive growth during SHT, and the dislocation density decreases significantly, leading to orange peel defect and low flow stress during compression tests, respectively. The grey-coloured specimens have larger columnar grains. After SHT, some grains undergo recrystallisation, but others still maintain the shape of the large columnar grains, and the dislocation density does not change significantly, resulting in surface oxidation with smooth surface after thermal-mechanical testing and 10–25 MPa (30–50%) higher flow stress compared to the silver-coloured specimens in compression tests.