Is it permissible to supplicate with ill intent against a colleague and a manager due to work pressure, and is that considered an excess in supplication?

The default is to believe your colleague regarding her excuses, unless there is clear evidence of her dishonesty. In such a case, she should be advised against it, and the danger of lying and negligence should be explained to her. If she does not desist, it is permissible to inform the authorities to mitigate the harm. It is not permissible to supplicate against her merely based on suspicion of lying. However, if you are certain of her injustice, then it is permissible to supplicate against her only to the extent of the injustice, such as: "O Allah, take my right from so-and-so," not with curses like paralysis or the like. The same applies to the manager: the default is not to wrong her, but if she wrongs you, then do not supplicate against her except to the extent of her injustice. It is better to be patient and refrain from supplicating, especially when the injustice is not confirmed. Advice should be given, and the seriousness of neglecting work and favoritism towards some people at the expense of others should be explained.