Ignitable liquid residue (ILR) samples play an important role in fire investigations. Similar to other types of forensic evidence, maintaining sample integrity depends on the prevention of cross-contamination during both storage and transport. This study examines cross-contamination in ILR samples on various sample matrices (gravel, soil, wood). After inducing leaks in a controlled environment, sample analysis by GC×GC-ToF MS allowed for sensitive detection and in-depth characterization of cross-contamination processes. The potential for false positive identification of ILR is notably present due to cross-contamination. Compound transmission for a mid-range ILR (gasoline), for instance, was detectable after a 1 h exposure, with a complete profile transfer occurring after 8 h regardless of the matrix type. Visual comparisons and uptake rate calculations further confirmed matrix interaction effects taking place in the form of inherent native compound interference and adsorbate–adsorbate interaction during transmission and extraction processes for soil and wood matrices. Chemometric analysis highlighted the advantage of employing statistical analysis when investigating samples under matrix interactions by identifying several statistically significant compounds for reliably differentiating cross-contamination from background and simulated positive samples in different volatility ranges and compound classes. Untargeted analysis tentatively identified three additional compounds of interest within compound classes not currently investigated in routine analysis. The resulting classification between background, contaminated, and simulated positive samples showed no potential for false positive ILR identification and improved false negative errors, as evidenced by classification confidences progressing from 88% for targeted and 93% for untargeted to 95% for a diagnostic ratio analysis of three ratios deployed in tandem.