Dear Jean-Baptiste,
This is not likely to happen frequently yet can certainly happen. The percentile bootstrap method that the software uses does not construct confidence intervals based on the original sample's estimate, but based only on bootstrap samples. Thus, if the majority of the bootstrap samples is different from the original sample, the bootstrap CI may not contain the estimate. There are alternatives for adjusting for skewness in the bootstrap distribution, but they are not implemented yet. And it is not clear whether the alternatives are always preferred over the percentile method. I’d like to suggest increasing the number of bootstrap samples. Also, although we provide the bootstrap Cl of SRMR (and other fit indexes), you may consider reporting the original sample's SRMR only and applying its suggested rule of thumb cutoffs.
Best,
Heungsun