low number of significant peaks for one contrast

I am using Diffbind to call differential peaks on an ATAC seq dataset of four conditions (AW, BW, B, and C), and each condition has 2 replicates. One of my replicates (BW2) has low quality (low number of peaks detected by MACS2 compared to the other replicate, and low FRiP).

I got very low number of significant peaks for the comparison BW x AW, and it is expected because of the low quality of one of the replicates. But why I get a high number of peaks for the other comparisons that include this low quality replicate? I am worried if there is any issue with the analysis. Any suggestions?

dbObj <- dba(sampleSheet=samples, minOverlap=2)
consensus <- dba.peakset(dbObj, consensus = DBA_CONDITION, minOverlap=2)
consensus <- dba(consensus, consensus$masks$Consensus, minOverlap=1)
consensus.peaks <- dba.peakset(consensus, bRetrieve=TRUE)
counts <- dba.count(dbObj, peaks=consensus.peaks)
contrast <- dba.contrast(counts, categories=DBA_FACTOR, minMembers = 2)
analysed.consensus <- dba.analyze(contrast, method=DBA_ALL_METHODS, bBlacklist=FALSE, bGreylist=FALSE)

My results are:

Design: [~Factor] | 6 Contrasts:
  Factor Group Samples Group2 Samples2
1 Factor    BW       2     AW        2
2 Factor    BW       2      C        2
3 Factor    BW       2     BT        2
4 Factor    AW       2      C        2
5 Factor    AW       2     BT        2
6 Factor    BT       2      C        2

8 Samples, 113008 sites in matrix:
   ID Factor Condition Replicate    Reads FRiP
1 BW1     BW        BW         1 18351704 0.21
2 BW2     BW        BW         2 23909409 0.07
3 AW1     AW        AW         1 27899970 0.11
4 AW2     AW        AW         2 27712756 0.15
5  C1      C         C         1 19207760 0.44
6  C2      C         C         2 38438952 0.46
7 BT1     BT        BT         1 35313077 0.35
8 BT2     BT        BT         2 33108371 0.35

Design: [~Factor] | 6 Contrasts:
  Factor Group Samples Group2 Samples2 DB.edgeR DB.DESeq2
1 Factor    BW       2     AW        2      125         0
2 Factor    BW       2      C        2    83426     81864
3 Factor    BW       2     BT        2    54819     56533
4 Factor    AW       2      C        2    88260     84513
5 Factor    AW       2     BT        2    60529     61937
6 Factor    BT       2      C        2    25749     19873