diff --git a/image_analysis/scale_merge/RotationScaleMerge.cpp b/image_analysis/scale_merge/RotationScaleMerge.cpp
index aa891fca2..e5e0e8d24 100644
--- a/image_analysis/scale_merge/RotationScaleMerge.cpp
+++ b/image_analysis/scale_merge/RotationScaleMerge.cpp
@@ -1206,14 +1206,14 @@ void RotationScaleMerge::BuildInRangeObservations(std::unique_ptr<SortKey[]> &ke
     ingest_zeta.reset(new float[n_keep]);
     if (x.GetBandwidthFWHM().value_or(0.0f) > 0.0f)
         ingest_d.reset(new float[n_keep]);
-    std::atomic<int64_t> n_resolved{0};
+    std::atomic<int64_t> n_resolved{0}, n_negative_var{0};
     partials.clear();
     partials.resize(n_keep);
     corr_ingested.resize(n_keep);
     ParallelFor(n_frames, nthreads, [&](int o) {
         int32_t src = src_start[o];
         int32_t at = frame_start[o];
-        int64_t resolved = 0;
+        int64_t resolved = 0, negative_var = 0;
         for (const auto &r : partials_out[o].reflections) {
             if (!keep[src]) { ++src; continue; }
             ++src;
@@ -1228,7 +1228,8 @@ void RotationScaleMerge::BuildInRangeObservations(std::unique_ptr<SortKey[]> &ke
             obs.frame = o;
             obs.corr = r.image_scale_corr;
             finite_ok[at] = (std::isfinite(r.I) && std::isfinite(obs.prescaling_corr) && obs.prescaling_corr != 0.0f
-                             && std::isfinite(r.sigma) && r.sigma > 0.0f) ? 1 : 0;
+                             && std::isfinite(r.sigma) && r.sigma > 0.0f && !(r.var_bkg < 0.0f)) ? 1 : 0;
+            negative_var += r.var_bkg < 0.0f;   // refused as in AcceptReflection
             ingest_delta_phi[at] = SmoothedDeltaPhi(sg, o, r.h, r.k, r.l, r.delta_phi_deg, resolved);
             ingest_partiality[at] = r.partiality;
             ingest_image_number[at] = r.image_number;
@@ -1238,6 +1239,7 @@ void RotationScaleMerge::BuildInRangeObservations(std::unique_ptr<SortKey[]> &ke
             ++at;
         }
         n_resolved += resolved;
+        n_negative_var += negative_var;
     });
 
     n_partials_obs = n_keep;
@@ -1245,6 +1247,9 @@ void RotationScaleMerge::BuildInRangeObservations(std::unique_ptr<SortKey[]> &ke
         logger->Info("Smoothed per-frame geometry over +-{} frames (chosen by cross-validation); "
                      "recomputed delta_phi for {} of {} partials", sg.half, n_resolved.load(), n_keep);
 
+    if (n_negative_var > 0)
+        logger->Info("RotationScaleMerge: {} observations left out - their background variance is below zero",
+                     n_negative_var.load());
     if (n_keep < n_obs)
         logger->Info("RotationScaleMerge: dropped {} of {} observations ({} of {} distinct hkl) outside the "
                     "requested resolution range - nothing downstream could have merged them",