Are these small crops and originally JPGs? The best reason, among many, reasons to shoot RAW is to preserve the original capture data and be able to make edits and conversions without every changing the original raw file. It appears that you saved these as JPGs which compresses them and tosses out a lot of data, then saved them again which further destroys data by compressing again. By 3 or 4 saves there is no fidelity left and the image is ruined. It is possible to get good JPG compression if the file is only converted once. If you need another size or additional edits, start with a new conversion of the original untouched file so every version of the edited version of an image is a first generation of conversion and saving as a JPG.
The photo of the bird is a good example of a number of better focus targets in the same focal point coverage area. The branch is a better target than the dark low contrast bird. Both were in the same focus sensor coverage area. If these were small crops, the bird was just too small in terms of defining pixel count to dominate the focal point. If his head filled the focal point, the camera would have been more likely to pick the same target as you did. Stan St Petersburg Russia