The article considers the reliability as one of the key characteristics of the software quality assurance. The analysis of the principles of taking into account secondary faults of software tools is carried out. The main provisions of the works are considered in which the parameters of imperfect debugging are investigated. The principles of the theory of dynamics of software systems are considered in view of account of secondary faults. The application of the theory of time series and simulation modeling for estimating the number of secondary faults of software is considered. The examples of different approaches to the modifications of the risk functions of software reliability evaluation models for the possibility of taking into account secondary faults are given on the example of the Jelinski-Moranda model. The possibility of combining modified models for assessing the reliability of software tools is analyzed in order to obtain an analytical expression for identifying the number of secondary faults. The application of exponential approximation and second-degree polynomial approximation of fault trend for estimating the number of secondary faults is considered. The analysis of advantages and disadvantages of the principles of taking into account secondary faults is carried out.